basic_classes.yaml

id: https://w3id.org/nmdc/basic_classes
name: NMDC-Basic-classes
title: NMDC Attribute Basic Types
description: Schema for National Microbiome Data Collaborative (NMDC), Basic Types

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

prefixes:
  linkml: https://w3id.org/linkml/
  EFO: http://www.ebi.ac.uk/efo/
  BFO: http://purl.obolibrary.org/obo/BFO_
  rdfs: http://www.w3.org/2000/01/rdf-schema#
  biolink: https://w3id.org/biolink/vocab/
  owl: http://www.w3.org/2002/07/owl#


imports:
  - external_identifiers # in cycle with attribute_values
  - mixs # in cycle with attribute_values


classes:

  NamedThing:
    class_uri: nmdc:NamedThing
    description: "a databased entity or concept/class"
    abstract: true
    slots:
      - id
      - name
      - description
      - alternative_identifiers
      - type

  OntologyClass:
    class_uri: nmdc:OntologyClass
    description: >-
      A representation of class defined in an external ontology.
    is_a: NamedThing
    slots:
      - alternative_names
    attributes:
      definition:
        range: string
        description: >-
          The definition of the ontology term as provided by the ontology.
      relations:
        range: OntologyRelation
        multivalued: true
        inlined_as_list: true
        inlined: true
    slot_usage:
      id:
        pattern: '^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$'
        notes:
          - The identifiers for terms from external ontologies can't have their ids constrained to the nmdc namespace
    exact_mappings:
      - biolink:OntologyClass
      - owl:Class
      - schema:Class

  OntologyRelation:
    aliases: ["OntologyAssociation"]
    description: >-
      A relationship between two ontology classes as specified either directly in the ontology in the form
      of axioms (statements or assertions that defines rules or constraints in an ontology) or inferred via
      reasoning.  The association object is defined by two terms (the subject and the object) and the relationship
      between them (the predicate). Because ontologies often have a plethora of relationships/axiom types and can have
      additional metadata on the relationship itself, these kinds of relationships are structured as a class instead
      of a simple set of slots on OntologyClass itself.
    comments: >-
      For example, the relationship between 'soil' and 'enriched soil' in the Environmental Ontology (ENVO)
      is defined by the following axioms: 'enriched soil' subclass_of 'soil', and 'enriched soil' 
      has_increased_levels_of (some) 'material entity.'  Converting these stat∂ements to OntologyAssociations 
      so they can be used in the NMDC data stores, the subject of the first axiom or statement, 
      would be 'soil', the predicate would be 'subclass_of', and the object would be 'enriched soil'.  For the second
      axiom, the subject would be 'enriched soil', the predicate would be 'has_increased_levels_of', and the object
      would be 'material entity.' (Note that text labels are used in this example for ease of understanding and 
      the literal values of subject, predicate, and object in this class will be the id (curie) of the 
      `OntologyClass` as defined below).  Not all ontology axioms (associations) between terms need to be 
      ingested into the NMDC data stores.  In general, subclass_of and part_of relationships/axioms are often 
      good default relations/associations to support ontology browsing in user interfaces.
    class_uri: nmdc:OntologyRelation
    slots:
      - type
    attributes:
      subject:
        range: OntologyClass
        required: true
      predicate:
        range: OntologyClass
        required: true
      object:
        range: OntologyClass
        required: true


  FailureCategorization:
    class_uri: nmdc:FailureCategorization
    slots:
      - qc_failure_what
      - qc_failure_where
      - type

  MaterialEntity:
    class_uri: nmdc:MaterialEntity
    abstract: true
    aliases:
      - Material
      - Physical entity
    is_a: NamedThing
    title: Material Entity
  Instrument:
    class_uri: nmdc:Instrument
    description: A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
    is_a: MaterialEntity
    slots:
      - vendor
      - model
    aliases:
      - device
    exact_mappings:
      - OBI:0000968
    slot_usage:
      id:
        structured_pattern:
          syntax: "{id_nmdc_prefix}:inst-{id_shoulder}-{id_blade}$"
          interpolated: true
  PlannedProcess:
    abstract: true
    class_uri: OBI:0000011
    is_a: NamedThing
    title: Planned Process
    slots:
      - has_input
      - has_output
      - processing_institution
      - protocol_link
      - start_date
      - end_date
      - qc_status
      - qc_comment
      - has_failure_categorization
  Protocol:
    class_uri: nmdc:Protocol
    slots:
      - url
      - name
      - type
  CreditAssociation:
    aliases:
      - study role
      - credit table
      - associated researchers
    description: >-
      This class supports binding associated researchers to studies.
      There will be at least a slot for a CRediT Contributor Role and for a person value.
      Specifically see the associated researchers tab on the NMDC_SampleMetadata-V4_CommentsForUpdates
      at https://docs.google.com/spreadsheets/d/1INlBo5eoqn2efn4H2P2i8rwRBtnbDVTqXrochJEAPko/edit#gid=0
    slots:
      - applies_to_person
      - applied_roles
      - type
    class_uri: prov:Association
    see_also:
      - https://casrai.org/credit/
  Doi:
    class_uri: nmdc:Doi
    aliases:
      - DOIs
      - digital object identifiers
    description: >-
      A centrally registered identifier symbol used to uniquely identify objects given by the International DOI Foundation.
      The DOI system is particularly used for electronic documents.
    exact_mappings:
      - OBI:0002110
    slots:
      - doi_value
      - doi_provider
      - doi_category
      - type
    rules:
      - title: dataset_award_dois_required
        description: >-
          If doi_category is a publication_doi, then doi_provider is not required. Otherwise, doi_provider is required.
        preconditions:
          slot_conditions:
            doi_category:
              any_of:
                - equals_string: dataset_doi
                - equals_string: award_doi
        postconditions:
          slot_conditions:
            doi_provider:
              required: true
  Study:
    class_uri: 'nmdc:Study'
    is_a: NamedThing
    aliases:
      - proposal
      - research proposal
      - research study
      - investigation
      - project
      - umbrella project
      - research initiative
    description: >-
      A study summarizes the overall goal of a research initiative and outlines the key objective of its underlying projects.
    comments: The Study class can include both consortia and research studies.
    alt_descriptions:
      embl.ena:
        A study (project) groups together data submitted to the archive and
        controls its release date. A study accession is typically used when citing
        data submitted to ENA
    slots:
      ## Alternative IDs
      - emsl_project_identifiers
      - gnps_task_identifiers
      - gold_study_identifiers
      - insdc_bioproject_identifiers
      - jgi_portal_study_identifiers
      - mgnify_project_identifiers
      - neon_study_identifiers

      ## Related IDs
      - related_identifiers

      - alternative_descriptions
      - alternative_names
      - alternative_titles

      - ecosystem
      - ecosystem_category
      - ecosystem_subtype
      - ecosystem_type
      - specific_ecosystem

      - associated_dois
      - funding_sources
      - has_credit_associations
      - homepage_website
      - notes
      - objective
      - part_of
      - principal_investigator
      - protocol_link
      - study_category
      - study_image
      - title
      - websites
    slot_usage:
      id:
        required: true
        structured_pattern:
          syntax: "{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$"
          interpolated: true
      name:
        annotations:
          tooltip: Provide a name for the study your samples will belong with.
      websites:
        annotations:
          tooltip:
            Link to the Principal Investigator's research lab webpage
            or the study webpage associated with this collection of samples.
            Multiple links can be provided.
      homepage_website:
        annotations:
          tooltip:
            Link to the consortium's homepage if the study_category is a consortium.
      description:
        description: A brief, link-free summary of a Study
        annotations:
          tooltip: Provide a brief description of your study.
        comments: Include links in other Study slots, such as websites or dois.
      notes:
        annotations:
          tooltip: Add any additional notes or comments about this study.
      alternative_identifiers:
        description: Unique identifier for a study submitted to additional resources. Matches that which has been submitted to NMDC
      alternative_names:
        annotations:
          tooltip:
            Project, study, or sample set names the are also associated with this submission
            or other names / identifiers for this study.
      related_identifiers:
        description: Unique identifier for a study submitted to additional resources. Similar, but not necessarily identical to that which has been submitted to NMDC
      insdc_bioproject_identifiers:
        description: Unique identifier for a bioproject submitted to INSDC that relates to the NMDC submitted study.
        annotations:
          tooltip: Provide the NCBI BioProject Accession Number associated with the listed NCBI BioProject Title.
      part_of:
        description: Links a study or consortium to a parent (or umbrella) study or consortium.
        comments:
          - Value is the id of the umbrella study or consortium.
        range: Study
        structured_pattern:
          syntax: "{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$"
          interpolated: true
      protocol_link:
        multivalued: true
        inlined_as_list: true
    exact_mappings:
      - OBI:0000066
      - SIO:000747
      - NCIT:C41198
      - ISA:Investigation
    broad_mappings:
      - prov:Activity
    todos:
      - determine how to get data values for submitted_to_insdc, investigation_type,
        experimental_factor
      - project_name is redundant with name, so excluding it
    notes:
      - "sample GOLD link https://bioregistry.io/gold:Gs0110115"
      - "sample insdc.srs link https://www.ebi.ac.uk/ena/browser/view/PRJEB45055 ?"
      - "sample mgnify link https://www.ebi.ac.uk/metagenomics/studies/MGYS00005757"
      - "GOLD, insdc.srs and mgnify are reasonable prefixes for alternative study identifiers, but no longer for the Study.id"

  InformationObject:
    abstract: true
    is_a: NamedThing
    class_uri: nmdc:InformationObject
    description: >-
      Any data or knowledge that reduces uncertainty or enhances understanding about a system, process, or entity.
    comments:
      - The direct subclasses of NamedThing should aggregate the relevant classes and make them uniform. PlannedProcess and MaterialEntity are clearly disjoint. Let's do the same thing for our modelling of things that don't consist of matter and aren't processes.
      - InformationObjects may include embedded data or links to external resources via the url slot
      - May appear as output from a process, inputs into a process, or both
      - All slots relating one class to a InformationObject should be is_a sub-properties of has_input or has_output,
        if they are multivalued or otherwise organized
      - Historically information about many classes has been inlined into the class. This is an alternative pattern.
    see_also:
      - nmdc:AttributeValue

  DataObject:
    class_uri: nmdc:DataObject
    is_a: InformationObject
    description:
      "An object that primarily consists of symbols that represent information.   Files,
      records, and omics data are examples of data objects."
    slots:
      - compression_type
      - data_category
      - data_object_type
      - file_size_bytes
      - insdc_experiment_identifiers
      - md5_checksum
      - url
      - was_generated_by
      - in_manifest
    slot_usage:
      name:
        required: true
      description:
        required: true
      id:
        required: true
        structured_pattern:
          syntax: "{id_nmdc_prefix}:dobj-{id_shoulder}-{id_blade}$"
          interpolated: true
      was_generated_by:
        structured_pattern:
          syntax: "^{id_nmdc_prefix}:(wfmag|wfmb|wfmgan|wfmgas|wfmsa|wfmp|wfmt|wfmtan|wfmtas|wfnom|wfrbt|wfrqc)-{id_shoulder}-{id_blade}{id_version}$|^{id_nmdc_prefix}:(omprc|dgms|dgns)-{id_shoulder}-{id_blade}$"
          interpolated: true
  DataGeneration:
    class_uri: nmdc:DataGeneration
    is_a: PlannedProcess
    abstract: true
    aliases:
      - OmicsProcessing
      - assay
      - omics assay
      - sequencing project
      - experiment
    description: >-
      The methods and processes used to generate omics data from a biosample or organism.
    alt_descriptions:
      embl.ena:
        An experiment contains information about a sequencing experiment including
        library and instrument details.
    slots:
      - add_date
      - analyte_category
      - associated_studies
      - instrument_used
      - mod_date
      - principal_investigator
    slot_usage:
      has_input:
        required: true
        range: Sample
        structured_pattern:
          syntax: "{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$"
          interpolated: true
      associated_studies:
        range: Study
        structured_pattern:
          syntax: "{id_nmdc_prefix}:(sty)-{id_shoulder}-{id_blade}$"
          interpolated:
            true
      has_output:
        range: DataObject
        structured_pattern:
          syntax: "{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$"
          interpolated:
            true
    broad_mappings:
      - OBI:0000070
      - ISA:Assay

  WorkflowExecution:
    abstract: true
    class_uri: nmdc:WorkflowExecution
    is_a: PlannedProcess
    aliases:
      - analysis
    comments:
      - Each instance of this (and all other) subclasses of WorkflowExecution is a distinct run with start and stop times, potentially with different inputs and outputs
    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:
      - ended_at_time
      - execution_resource
      - git_url
      - started_at_time
      - version
      - was_informed_by
    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
      git_url:
        required: true
      has_input:
        required: true
        structured_pattern:
          syntax: "{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$"
          interpolated: true
      has_output:
        structured_pattern:
          syntax: "{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$"
          interpolated: true
      execution_resource:
        required: true
      was_informed_by:
        required: true
slots:
  associated_studies:
    description: The study associated with a resource.
    range: Study
    multivalued: true
    structured_pattern:
      syntax: "{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$"
      interpolated: true
    required: true
  part_of:
    aliases:
      - is part of
    range: NamedThing
    multivalued: true
    slot_uri: dcterms:isPartOf
    description: Links a resource to another resource that either logically or physically includes it.
  was_informed_by:
    range: DataGeneration
    mappings:
      - prov:wasInformedBy
    structured_aliases:
      was_informed_by:
        contexts:
        -  https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml
        predicate: EXACT_SYNONYM
  principal_investigator:
    aliases:
      - PI
    range: PersonValue
    description: Principal Investigator who led the study and/or generated the dataset.
  was_generated_by:
    range: WorkflowExecution
    mappings:
      - prov:wasGeneratedBy
    any_of:
      - range: WorkflowExecution
      - range: DataGeneration
  associated_dois:
    description: A list of DOIs associated with a resource, such as a list of DOIS associated with a Study.
    aliases:
      - Associated DOIs
      - Associated digital object identifiers
    range: Doi
    multivalued: true
    inlined_as_list: true
    examples:
      value:
        - doi: doi:10.46936/intm.proj.2021.60141/60000423
          doi_provider: emsl
          doi_category: award_doi
        - doi: doi:10.1101/2022.12.12.520098
          doi_category: publication_doi
        - doi: doi:10.48321/D1Z60Q
          doi_category: data_management_plan_doi
          doi_provider: gsc
      description: Provides a list of two DOIs; specifically, an EMSL award DOI and a publication DOI.
  has_credit_associations:
    range: CreditAssociation
    multivalued: true
    inlined_as_list: true
    description:
      "This slot links a study to a credit association.  The credit association
      will be linked to a person value and to a CRediT Contributor Roles term. Overall
      semantics: person should get credit X for their participation in the study"
    slot_uri: prov:qualifiedAssociation
    annotations:
      tooltip: Other researchers associated with this study.
  protocol_link:
    range: Protocol
  study_category:
    description: The type of research initiative
    range: StudyCategoryEnum
    required: true
  study_image:
    range: ImageValue
    multivalued: true
    inlined_as_list: true
    description: Links a study to one or more images.
  applies_to_person:
    range: PersonValue
    required: true
  applied_roles:
    range: CreditEnum
    multivalued: true
    required: true
    annotations:
      tooltip: >-
        Identify all CRediT roles associated with this contributor. CRediT Information: https://info.orcid.org/credit-for-research-contribution ; CRediT: https://credit.niso.org/

  has_input:
    aliases:
      - input
    range: NamedThing
    multivalued: true
    description: >-
      An input to a process.

  has_output:
    aliases:
      - output
    range: NamedThing
    multivalued: true
    description: An output from a process.

  instrument_used:
    range: Instrument
    multivalued: true
    description: What instrument was used during DataGeneration or MaterialProcessing.

  in_manifest:
    range: Manifest
    multivalued: true
    description: one or more combinations of other DataObjects that can be analyzed together
    comments:
      - A DataObject can be part of multiple manifests, for example, a DataObject could be part of a manifest for a single run of an instrument and a manifest for technical replicates of a single sample.
    structured_pattern:
      syntax: "^{id_nmdc_prefix}:manif-{id_shoulder}-{id_blade}$"
      interpolated: true  

  manifest_category:
    range: ManifestCategoryEnum
    description: >-
      The type of context in which the constituent DataObjects can be analyzed together.
    required: true

  model:
    range: InstrumentModelEnum
  vendor:
    range: InstrumentVendorEnum

  qc_failure_where:
    range: FailureWhereEnum
    description: >-
      Describes the nmdc schema class that corresonds to where the failure occurred.
      Most commonly this would be the same as Class that generated the results.
    comments:
      - If the assembly size was too small to proceed to annotation failure_where would be MetagenomeAssembly.

  qc_failure_what:
    range: FailureWhatEnum
    description: >-
      Provides a summary about what caused a lab or workflow process to fail
    comments:
      - For example, low read count from a sequencer, malformed fastq files, etc.

enums:
  CreditEnum:
    permissible_values:
      Conceptualization:
        description: Conceptualization
      Data curation:
        description: Data curation
      Formal Analysis:
        description: Formal Analysis
      Funding acquisition:
        description: Funding acquisition
      Investigation:
        description: Investigation
      Methodology:
        description: Methodology
      Project administration:
        description: Project administration
      Resources:
        description: Resources
      Software:
        description: Software
      Supervision:
        description: Supervision
      Validation:
        description: Validation
      Visualization:
        description: Visualization
      Writing original draft:
        description: "Writing \u2013 original draft"
      Writing review and editing:
        description: "Writing \u2013 review & editing"
      Principal Investigator:
        description: principal investigator role
        meaning: OBI:0000103
      Submitter:
        description: the person(s) who enter study and biosample metadata into the NMDC submission portal
        meaning: EFO:0001741
    comments:
      - CreditEnums come from https://casrai.org/credit/
  StudyCategoryEnum:
    permissible_values:
      research_study:
        description: A detailed examination, analysis, or critical inspection of a hypothesis-driven experiment.
        exact_mappings:
          - SIO:001066
          - NCIT:C63536
          - ISA:Study
        close_mappings:
          - OBI:0000355
      consortium:
        description: >-
          A group formed to undertake a venture that is beyond the capabilities of the individual members. Each member of the
          consortium brings a high level of expertise in a specific area to ensure the successful completion of the project.
        comments: A consortium has collections of data, those data do not come from a hypothesis-driven experiment.
        exact_mappings:
          - NCIT:C61538
  
  ManifestCategoryEnum:
    description: A list of contexts in which some DataObjects can be analyzed together.
    permissible_values:
      instrument_run:
        description: >-
          A collection of data objects from a single run of an instrument.
      poolable_replicates:
        description: >-
          A collection of data objects that can be pooled for downstream analyses.
      fractions:
        description: >-
          A collection of data objects that represent fractions of a single sample.

  InstrumentModelEnum:
    permissible_values:
      exploris_21T:
        aliases:
          - Exploris 21T

      exploris_240:
        aliases:
          - Orbitrap Exploris 240

      exploris_480:
        aliases:
          - Orbitrap Exploris 480

      ltq_orbitrap_velos:
        aliases:
          - LTQ Orbitrap Velos
          - LTQ Orbitrap Velos ETD
          - Velos

      orbitrap_fusion_lumos:
        aliases:
          - Orbitrap Fusion Lumos
          - Fusion

      orbitrap_eclipse_tribid:
        aliases:
          - Orbitrap Eclipse Tribid
          - Eclipse

      orbitrap_q_exactive:
        aliases:
          - Orbitrap Q-Exactive HF
          - Orbitrap Q-Exactive HF-X

      solarix_7T:
        aliases:
          - 7T Solarix
          - 7T FT-ICR MS
          - 7T MRMS

      solarix_12T:
        aliases:
          - 12T Solarix
          - 12T FT-ICR MS
          - 12T MRMS

      solarix_15T:
        aliases:
          - 15T Solarix
          - 15T FT-ICR MS
          - 15T MRMS

      agilent_8890A:
        aliases:
          - 8890A GC-MS
          - Agilent GC MS

      agilent_7980A:
        aliases:
          - 7980A GC-MS
          - Agilent GC MS

      vortex_genie_2:
        aliases:
          - VortexGenie2
          
      novaseq:
        aliases:
          - NovaSeq
          - Illumina NovaSeq
          
      novaseq_6000:
        aliases:
          - NovaSeq 6000
          - Illumina NovaSeq 6000
        meaning: OBI:0002630
        comments: Possible flowcell versions are SP, S1, S2, S4.
        see_also: 
         - https://www.illumina.com/systems/sequencing-platforms/novaseq/specifications.html
        structured_aliases:
          Illumina NovaSeq S2:
            contexts:
            -  https://gold.jgi.doe.gov/
            predicate: NARROW_SYNONYM
          Illumina NovaSeq S4:
            contexts:
            -  https://gold.jgi.doe.gov/
            predicate: NARROW_SYNONYM    
          Illumina NovaSeq SP:
            contexts:
            -  https://gold.jgi.doe.gov/
            predicate: NARROW_SYNONYM                

      novaseq_x:
        aliases:
          - Illumina NovaSeq X
          - Illumina NovaSeq X Plus 
        comments: Possible flowcell versions are 1.5B, 10B, 25B. Only difference between X and X Plus is 2 flowcells for X Plus versus 1 flowcell for X.
        see_also: 
          - https://www.illumina.com/systems/sequencing-platforms/novaseq-x-plus/specifications.html
      
      hiseq:
        aliases:
          - Illumina HiSeq
      
      hiseq_1000:
        aliases:
          - Illumina HiSeq 1000
        meaning: OBI:0002022
      
      hiseq_1500:
        aliases:
          - Illumina HiSeq 1500
        meaning: OBI:0003386
      
      hiseq_2000:
        aliases:
          - Illumina HiSeq 2000
        meaning: OBI:0002001
     
      hiseq_2500:
        aliases:
          - Illumina HiSeq 2500
        meaning: OBI:0002002
        structured_aliases:
          Illumina HiSeq 2500-1TB:
            contexts:
            -  https://gold.jgi.doe.gov/
            predicate: NARROW_SYNONYM
          Illumina HiSeq 2500-Rapid:
            contexts:
            -  https://gold.jgi.doe.gov/
            predicate: NARROW_SYNONYM    
      
      hiseq_3000:
        aliases:
          - Illumina HiSeq 3000
        meaning: OBI:0002048
      
      hiseq_4000:
        aliases:
          - Illumina HiSeq 4000
        meaning: OBI:0002049
     
      hiseq_x_ten:
        aliases:
          - Illumina HiSeq X Ten
        meaning: OBI:0002129
      
      miniseq:
        aliases:
          - Illumina MiniSeq
        meaning: OBI:0003114
           
      miseq:
        aliases:
          - MiSeq
          - Illumina MiSeq
        meaning: OBI:0002003
        
      nextseq_1000:
        aliases:
          - Illumina NextSeq 1000
        meaning: OBI:0003606
        
      nextseq:
        aliases:
          - NextSeq
          - Illumina NextSeq
        structured_aliases:
          Illumina NextSeq-HO:
           contexts:
            -  https://gold.jgi.doe.gov/
           predicate: NARROW_SYNONYM
          Illumina NextSeq-MO:
            contexts:
            -  https://gold.jgi.doe.gov/
            predicate: NARROW_SYNONYM              
      
      nextseq_500:
        aliases:
          - NextSeq 500
          - Illumina NextSeq 500
        meaning: OBI:0002021
      
      nextseq_550:
        aliases:
          - NextSeq 550
          - Illumina NextSeq 550
        meaning: OBI:0003387
      
      gridion:
        aliases:
          - Oxford Nanopore GridION Mk1
        meaning: OBI:0002751
      
      minion:
        aliases:
          - Oxford Nanopore MinION
        meaning: OBI:0002750
      
      promethion:
        aliases:
          - Oxford Nanopore PromethION
        meaning: OBI:0002752
      
      rs_II:
        aliases:
          - PacBio RS II
        meaning: OBI:0002012
      
      sequel:
        aliases:
          - PacBio Sequel
        meaning: OBI:0002632
      
      sequel_II:
        aliases:
          - PacBio Sequel II
        meaning: OBI:0002633
      
      revio:
        aliases:
          - PacBio Revio
          - Revio

  InstrumentVendorEnum:
    permissible_values:
      waters:
        aliases:
          - Waters Corporation
      agilent:
        aliases:
          - Agilent Technologies
      bruker:
        aliases:
          - Bruker Corporation
          - Bruker Daltonics
      thermo_fisher:
        aliases:
          - ThermoFisher
          - Thermo Fisher Scientific
      vwr:
      perkin_elmer:
      gilson:
      scientific_industries:
      illumina:
        aliases:
          - Illumina
        meaning: OBI:0000759
      pacbio:
        aliases:
          - PacBio
          - Pacific Biosciences
        meaning: OBI:0001856
      oxford_nanopore:
        aliases:
          - Oxford Nanopore Technologies
        meaning: OBI:0002755
      pnnl:
        aliases:
          - PNNL
  FailureWhatEnum:
    description: The permitted values for describing where a failure occurred during processing in the lab during analysis workflows.
    permissible_values:
      low_read_count:
        description: Number of output reads is not sufficient to continue to the next analysis step.
      malformed_data:
        description: Workflow failure reading input or writing the output file(s).
      assembly_size_too_small:
        description: The size of the metagenome or metatranscriptome assembly is too small to proceed to the next analysis workflow.
      no_valid_data_generated:
        description: A process ran but did not produce any output. Ie binning ran but did not produce any medium or high quality bins.
      other:
        description: A lab process or analysis workflow has failed in a way that has not been captured by the available values yet. Please use slot 'qc_comment' to specify details.

  FailureWhereEnum:
    description: The permitted values for describing where in the process, either a lab or analysis workflow step, the failure occurred.
    comments:
      - At Chris' recommendation permissible values for this enumeration are the same as Class names.
    permissible_values:
      NucleotideSequencing:
        description: A failure has occurred during nucleotide sequencing, a data generation process.
      MassSpectrometry:
        description: A failure has occurred during mass spectrometry, a data generation process.
      Pooling:
        description: A failure has occurred in pooling, a lab process.
      Extraction:
        description: A failure has occurred in extraction, a lab process.
      LibraryPreparation:
        description: A failure has occurred in library preparation, a lab process.
      MetagenomeAssembly:
        description: A failure has occurred in metagenome assembly, a workflow process.
      MetatranscriptomeExpressionAnalysis:
        description: A failure has occurred in metatranscriptome expression analysis, a workflow process.
      MagsAnalysis:
        description: A failure has occurred in binning, a workflow process to generate metagenome-assembled genomes (MAGS).
      ReadQcAnalysis:
        description: A failure has occurred in read qc, a workflow process.
      ReadBasedTaxonomyAnalysis:
        description: A failure has occurred in reads based taxonomy, a workflow process.
      MetagenomeAnnotation:
        description: A failure has occurred in annotation, a workflow process.
      MetatranscriptomeAssembly:
        description: A failure has occurred in assembly, a workflow process.
      MetatranscriptomeAnnotation:
        description: A failure has occurred in annotation, a workflow process.
      MetabolomicsAnalysis:
        description: A failure has occurred in analyzing metabolomics data.
      MetaproteomicsAnalysis:
        description: A failure has occurred in analyzing metaproteomics data.
      NomAnalysis:
        description: A failure has occurred in analyzing NOM data.