workflow_execution_activity.yaml

id: https://w3id.org/nmdc/workflow_execution_activity
name: NMDC-Workflow-Execution
title: Workflow Execution Activities module for NMDC Schema

license: https://creativecommons.org/publicdomain/zero/1.0/

notes:
  - "should type be required for WorkflowExecutionActivity ?  What would the range be ?"

imports:
  - core

prefixes:
  nmdc: https://w3id.org/nmdc/
  linkml: https://w3id.org/linkml/

default_prefix: nmdc
default_range: string

subsets:
  workflow subset:
    description: >-
      Subset consisting of just the workflow execution activities

classes:

  WorkflowExecutionActivity:
    aliases:
      - analysis
    comments:
      - Each instance of this (and all other) activities is  a distinct run with start and stop times, potentially with different inputs and outputs
    is_a: Activity
    in_subset:
      - workflow subset
    description: >-
      Represents an instance of an execution of a particular workflow
    alt_descriptions:
      embl.ena: >-
        An analysis contains secondary analysis results derived from sequence reads (e.g. a genome assembly)
    slots:
      - execution_resource
      - git_url
      - has_input
      - has_output
      - part_of
      - type
      - version
      - qc_status
      - qc_comment
      - has_failure_categorization
    rules:
      - title: qc_status_pass_has_output_required
        description: >-
          If qc_status has a value of pass, then the has_output slot is required.
        preconditions:
          slot_conditions:
            qc_status:
              equals_string: pass
        postconditions:
          slot_conditions:
            has_output:
              required: true
      - title: qc_status_pass_null_has_output_required
        description: >-
          If qc_status is not specified, then the has_output slot is required.
        preconditions:
          slot_conditions:
            qc_status:
              value_presence: ABSENT
        postconditions:
          slot_conditions:
            has_output:
              required: true
          
    slot_usage:
      started_at_time:
        required: true
      ended_at_time:
        required: true
      git_url:
        required: true
      has_input:
        required: true
      # has_output:
      #   required: true
      execution_resource:
        required: true
      type:
        required: true
      id:
        required: true
        structured_pattern:
          syntax: "{id_nmdc_prefix}:wf-{id_shoulder}-{id_blade}{id_version}{id_locus}"
          interpolated: true


  MetagenomeAssembly:
    description: A workflow execution activity that converts sequencing reads into an assembled metagenome.
    comments:
      - instances of this class may use a de novo assembly strategy in most or all cases relevant to NMDC
    is_a: WorkflowExecutionActivity
    in_subset:
      - workflow subset
    slots:
      - type
      - asm_score
      - scaffolds
      - scaf_logsum
      - scaf_powsum
      - scaf_max
      - scaf_bp
      - scaf_n50
      - scaf_n90
      - scaf_l50
      - scaf_l90
      - scaf_n_gt50k
      - scaf_l_gt50k
      - scaf_pct_gt50k
      - contigs
      - contig_bp
      - ctg_n50
      - ctg_l50
      - ctg_n90
      - ctg_l90
      - ctg_logsum
      - ctg_powsum
      - ctg_max
      - gap_pct
      - gc_std
      - gc_avg
      - num_input_reads
      - num_aligned_reads
      - insdc_assembly_identifiers
    slot_usage:
      id:
        required: true
        structured_pattern:
          syntax: "{id_nmdc_prefix}:wfmgas-{id_shoulder}-{id_blade}{id_version}{id_locus}"
          interpolated: true

  MetatranscriptomeAssembly:
    is_a: WorkflowExecutionActivity
    in_subset:
      - workflow subset
    slots:
      - asm_score
      - scaffolds
      - scaf_logsum
      - scaf_powsum
      - scaf_max
      - scaf_bp
      - scaf_n50
      - scaf_n90
      - scaf_l50
      - scaf_l90
      - scaf_n_gt50k
      - scaf_l_gt50k
      - scaf_pct_gt50k
      - contigs
      - contig_bp
      - ctg_n50
      - ctg_l50
      - ctg_n90
      - ctg_l90
      - ctg_logsum
      - ctg_powsum
      - ctg_max
      - gap_pct
      - gc_std
      - gc_avg
      - num_input_reads
      - num_aligned_reads
      - insdc_assembly_identifiers
    slot_usage:
      id:
        required: true
        structured_pattern:
          syntax: "{id_nmdc_prefix}:wfmtas-{id_shoulder}-{id_blade}{id_version}{id_locus}"
          interpolated: true

  MetagenomeAnnotationActivity:
    description: A workflow execution activity that provides functional and structural annotation of assembled metagenome contigs
    is_a: WorkflowExecutionActivity
    slots:
      - type
      - gold_analysis_project_identifiers
    in_subset:
      - workflow subset
    slot_usage:
      id:
        required: true
        structured_pattern:
          syntax: "{id_nmdc_prefix}:wfmgan-{id_shoulder}-{id_blade}{id_version}{id_locus}"
          interpolated: true

  MetatranscriptomeAnnotationActivity:
    is_a: WorkflowExecutionActivity
    slots:
      - type
      - gold_analysis_project_identifiers
    in_subset:
      - workflow subset
    slot_usage:
      id:
        required: true
        structured_pattern:
          syntax: "{id_nmdc_prefix}:wfmtan-{id_shoulder}-{id_blade}{id_version}{id_locus}"
          interpolated: true

  MetatranscriptomeActivity:
    is_a: WorkflowExecutionActivity
    description: >-
      A metatranscriptome activity that e.g. pools assembly and annotation activity.
    in_subset:
      - workflow subset
    slots:
      - type
    slot_usage:
      id:
        required: true
        structured_pattern:
          syntax: "{id_nmdc_prefix}:wfmt-{id_shoulder}-{id_blade}{id_version}{id_locus}"
          interpolated: true


  MagsAnalysisActivity:
    description: A workflow execution activity that uses computational binning tools to group assembled contigs into genomes
    title: Metagenome-Assembled Genome analysis activity
    is_a: WorkflowExecutionActivity
    in_subset:
      - workflow subset
    slots:
      - type
      - input_contig_num
      - binned_contig_num
      - too_short_contig_num
      - low_depth_contig_num
      - unbinned_contig_num
      - mags_list
    slot_usage:
      id:
        required: true
        structured_pattern:
          syntax: "{id_nmdc_prefix}:wfmag-{id_shoulder}-{id_blade}{id_version}{id_locus}"
          interpolated: true


  MetagenomeSequencingActivity:
    description: Initial sequencing activity that precedes any analysis.  This activity has output(s) that are the raw sequencing data.
    title: Metagenome sequencing activity
    is_a: WorkflowExecutionActivity
    in_subset:
      - workflow subset
    slot_usage:
      id:
        required: true
        structured_pattern:
          syntax: "{id_nmdc_prefix}:wfmsa-{id_shoulder}-{id_blade}{id_version}{id_locus}"
          interpolated: true


  ReadQcAnalysisActivity:
    description: A workflow execution activity that performs quality control on raw Illumina reads including quality trimming, artifact removal, linker trimming, adapter trimming, spike-in removal, and human/cat/dog/mouse/microbe contaminant removal
    title: Read quality control analysis activity
    is_a: WorkflowExecutionActivity
    in_subset:
      - workflow subset
    slots:
      - type
      - input_read_count
      - input_base_count
      - output_read_count
      - output_base_count
      - input_read_bases
      - output_read_bases
      - version
    slot_usage:
      id:
        required: true
        structured_pattern:
          syntax: "{id_nmdc_prefix}:wfrqc-{id_shoulder}-{id_blade}{id_version}{id_locus}"
          interpolated: true

  ReadBasedTaxonomyAnalysisActivity:
    description: A workflow execution activity that performs taxonomy classification using sequencing reads
    title: Read based analysis activity
    is_a: WorkflowExecutionActivity
    in_subset:
      - workflow subset
    slots:
      - type
    slot_usage:
      id:
        required: true
        structured_pattern:
          syntax: "{id_nmdc_prefix}:wfrbt-{id_shoulder}-{id_blade}{id_version}{id_locus}"
          interpolated: true


  MetabolomicsAnalysisActivity:
    is_a: WorkflowExecutionActivity
    in_subset:
      - workflow subset
    slots:
      - has_calibration
      - has_metabolite_quantifications
    slot_usage:
      id:
        required: true
        structured_pattern:
          syntax: "{id_nmdc_prefix}:wfmb-{id_shoulder}-{id_blade}{id_version}{id_locus}"
          interpolated: true

  MetaproteomicsAnalysisActivity:
    is_a: WorkflowExecutionActivity
    in_subset:
      - workflow subset
    slots:
      - has_peptide_quantifications
    slot_usage:
      used:
        description: The instrument used to collect the data used in the analysis
      id:
        required: true
        structured_pattern:
          syntax: "{id_nmdc_prefix}:wfmp-{id_shoulder}-{id_blade}{id_version}{id_locus}"
          interpolated: true

  NomAnalysisActivity:
    is_a: WorkflowExecutionActivity
    in_subset:
      - workflow subset
    slots:
      - has_calibration
    slot_usage:
      used:
        range: string
        description: The instrument used to collect the data used in the analysis
      id:
        required: true
        structured_pattern:
          syntax: "{id_nmdc_prefix}:wfnom-{id_shoulder}-{id_blade}{id_version}{id_locus}"
          interpolated: true


slots:

  metagenome_assembly_parameter:
    abstract: true

  has_peptide_quantifications:
    domain: MetaproteomicsAnalysisActivity
    range: PeptideQuantification
    multivalued: true

  asm_score:
    is_a: metagenome_assembly_parameter
    description: >-
      A score for comparing metagenomic assembly quality from same sample.
    range: float

  scaffolds:
    is_a: metagenome_assembly_parameter
    description: >-
      Total sequence count of all scaffolds.
    range: float

  scaf_logsum:
    is_a: metagenome_assembly_parameter
    description: >-
      The sum of the (length*log(length)) of all scaffolds, times some constant.  Increase the contiguity, the score will increase
    range: float

  scaf_powsum:
    is_a: metagenome_assembly_parameter
    description: >-
      Powersum of all scaffolds is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).
    range: float

  scaf_max:
    is_a: metagenome_assembly_parameter
    description: >-
      Maximum scaffold length.
    range: float

  scaf_bp:
    is_a: metagenome_assembly_parameter
    description: >-
      Total size in bp of all scaffolds.
    range: float

  scaf_n50:
    is_a: metagenome_assembly_parameter
    description: >-
      Given a set of scaffolds, each with its own length, the N50 count is defined as the smallest number of scaffolds whose length sum makes up half of genome size.
    range: float

  scaf_n90:
    is_a: metagenome_assembly_parameter
    description: >-
      Given a set of scaffolds, each with its own length, the N90 count is defined as the smallest number of scaffolds whose length sum makes up 90% of genome size.
    range: float

  scaf_l50:
    is_a: metagenome_assembly_parameter
    description: >-
      Given a set of scaffolds, the L50 is defined as the sequence length of the shortest scaffold at 50% of the total genome length.
    range: float

  scaf_l90:
    is_a: metagenome_assembly_parameter
    description: >-
      The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all scaffolds of that length or longer contains at least 90% of the sum of the lengths of all scaffolds.
    range: float

  scaf_n_gt50k:
    is_a: metagenome_assembly_parameter
    description: >-
      Total sequence count of scaffolds greater than 50 KB.
    range: float

  scaf_l_gt50k:
    is_a: metagenome_assembly_parameter
    description: >-
      Total size in bp of all scaffolds greater than 50 KB.
    range: float

  scaf_pct_gt50k:
    is_a: metagenome_assembly_parameter
    description: >-
      Total sequence size percentage of scaffolds greater than 50 KB.
    range: float

  contigs:
    is_a: metagenome_assembly_parameter
    description: >-
      The sum of the (length*log(length)) of all contigs, times some constant.  Increase the contiguity, the score will increase
    range: float

  contig_bp:
    is_a: metagenome_assembly_parameter
    description: >-
      Total size in bp of all contigs.
    range: float

  ctg_n50:
    is_a: metagenome_assembly_parameter
    description: >-
      Given a set of contigs, each with its own length, the N50 count is defined as the smallest number_of_contigs whose length sum makes up half of genome size.
    range: float

  ctg_l50:
    is_a: metagenome_assembly_parameter
    description: >-
      Given a set of contigs, the L50 is defined as the sequence length of the shortest contig at 50% of the total genome length.
    range: float

  ctg_n90:
    is_a: metagenome_assembly_parameter
    description: >-
      Given a set of contigs, each with its own length, the N90 count is defined as the smallest number of contigs whose length sum makes up 90% of genome size.
    range: float

  ctg_l90:
    is_a: metagenome_assembly_parameter
    description: >-
      The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all contigs of that length or longer contains at least 90% of the sum of the lengths of all contigs.
    range: float

  ctg_logsum:
    is_a: metagenome_assembly_parameter
    description: >-
      Maximum contig length.
    range: float

  ctg_powsum:
    is_a: metagenome_assembly_parameter
    description: >-
      Powersum of all contigs is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).
    range: float

  ctg_max:
    is_a: metagenome_assembly_parameter
    description: >-
      Maximum contig length.
    range: float

  gap_pct:
    is_a: metagenome_assembly_parameter
    description: >-
      The gap size percentage of all scaffolds.
    range: float

  gc_std:
    is_a: metagenome_assembly_parameter
    description: >-
      Standard deviation of GC content of all contigs.
    range: float

  gc_avg:
    is_a: metagenome_assembly_parameter
    description: >-
      Average of GC content of all contigs.
    range: float

  num_input_reads:
    is_a: metagenome_assembly_parameter
    description: >-
      The sequence count number of input reads for assembly.
    range: float

  num_aligned_reads:
    is_a: metagenome_assembly_parameter
    description: >-
      The sequence count number of input reads aligned to assembled contigs.
    range: float

  read_qc_analysis_statistic:
    abstract: true

  mags_list:
    domain: MagsAnalysisActivity
    range: MagBin
    multivalued: true

  too_short_contig_num:
    range: integer

  binned_contig_num:
    range: integer

  input_contig_num:
    range: integer

  unbinned_contig_num:
    range: integer

  low_depth_contig_num:
    range: integer

  input_read_count:
    is_a: read_qc_analysis_statistic
    description: >-
      The sequence count number of input reads for QC analysis.
    range: float

  input_base_count:
    is_a: read_qc_analysis_statistic
    description: >-
      The nucleotide base count number of input reads for QC analysis.
    range: float

  output_read_count:
    is_a: read_qc_analysis_statistic
    description: >-
      After QC analysis sequence count number.
    range: float

  output_base_count:
    is_a: read_qc_analysis_statistic
    description: >-
      After QC analysis nucleotide base count number.
    range: float

  output_read_bases:
    range: float
    description: >-
      TODO

  input_read_bases:
    range: float
    description: >-
      TODO      

  has_calibration:
    range: string
    description: >-
      A reference to a file that holds calibration information.

  has_metabolite_quantifications:
    domain: MetabolomicsAnalysisActivity
    range: MetaboliteQuantification
    multivalued: true

  version:
    domain: Activity
    range: string