Class: LibraryPreparation

name: LibraryPreparation
comments:
- OBI:0000711 specifies a DNA input (but not ONLY a DNA input)
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- LibraryConstruction
close_mappings:
- OBI:0000711
is_a: MaterialProcessing
slots:
- is_stranded
- library_preparation_kit
- library_type
- nucl_acid_amp
- pcr_cond
- pcr_cycles
- pcr_primers
- stranded_orientation
- target_gene
- target_subfragment
- library_selection
- library_strategy
- library_source
- lib_layout
- adapters
slot_usage:
  has_input:
    name: has_input
    required: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'
      interpolated: true
  has_output:
    name: has_output
    required: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'
      interpolated: true
  id:
    name: id
    required: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:libprp-{id_shoulder}-{id_blade}$'
      interpolated: true
  pcr_cond:
    name: pcr_cond
    description: Description of reaction conditions and components of polymerase chain
      reaction performed during library preparation
class_uri: nmdc:LibraryPreparation

name: LibraryPreparation
comments:
- OBI:0000711 specifies a DNA input (but not ONLY a DNA input)
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- LibraryConstruction
close_mappings:
- OBI:0000711
is_a: MaterialProcessing
slot_usage:
  has_input:
    name: has_input
    required: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'
      interpolated: true
  has_output:
    name: has_output
    required: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'
      interpolated: true
  id:
    name: id
    required: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:libprp-{id_shoulder}-{id_blade}$'
      interpolated: true
  pcr_cond:
    name: pcr_cond
    description: Description of reaction conditions and components of polymerase chain
      reaction performed during library preparation
attributes:
  is_stranded:
    name: is_stranded
    description: Is the (RNA) library stranded or non-stranded (unstranded).
    comments:
    - A value of true means the library is stranded, flase means non-stranded.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    owner: LibraryPreparation
    domain_of:
    - LibraryPreparation
    range: boolean
  library_preparation_kit:
    name: library_preparation_kit
    from_schema: https://w3id.org/nmdc/nmdc
    exact_mappings:
    - GENEPIO:0001450
    rank: 1000
    owner: LibraryPreparation
    domain_of:
    - LibraryPreparation
    range: string
  library_type:
    name: library_type
    title: library type
    examples:
    - value: DNA
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    owner: LibraryPreparation
    domain_of:
    - LibraryPreparation
    range: LibraryTypeEnum
  nucl_acid_amp:
    name: nucl_acid_amp
    description: A link to a literature reference, electronic resource or a standard
      operating procedure (SOP), that describes the enzymatic amplification (PCR,
      TMA, NASBA) of specific nucleic acids
    title: nucleic acid amplification
    examples:
    - value: https://phylogenomics.me/protocols/16s-pcr-protocol/
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    slot_uri: MIXS:0000038
    owner: LibraryPreparation
    domain_of:
    - LibraryPreparation
    range: TextValue
    structured_pattern:
      syntax: ^({PMID}|{DOI}|{URL})$
      interpolated: true
      partial_match: true
  pcr_cond:
    name: pcr_cond
    annotations:
      Expected_value:
        tag: Expected_value
        value: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final
          elongation:degrees_minutes;total cycles
    description: Description of reaction conditions and components of polymerase chain
      reaction performed during library preparation
    title: pcr conditions
    examples:
    - value: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35
    - value: initial denaturation:94degC_1.5min
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    keywords:
    - condition
    - pcr
    string_serialization: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final
      elongation:degrees_minutes;total cycles
    slot_uri: MIXS:0000049
    owner: LibraryPreparation
    domain_of:
    - LibraryPreparation
    range: string
  pcr_cycles:
    name: pcr_cycles
    from_schema: https://w3id.org/nmdc/nmdc
    exact_mappings:
    - OBI:0002475
    rank: 1000
    owner: LibraryPreparation
    domain_of:
    - LibraryPreparation
    range: integer
  pcr_primers:
    name: pcr_primers
    description: PCR primers that were used to amplify the sequence of the targeted
      gene, locus or subfragment. This field should contain all the primers used for
      a single PCR reaction if multiple forward or reverse primers are present in
      a single PCR reaction. The primer sequence should be reported in uppercase letters
    title: pcr primers
    examples:
    - value: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    keywords:
    - pcr
    slot_uri: MIXS:0000046
    owner: LibraryPreparation
    domain_of:
    - LibraryPreparation
    range: string
    structured_pattern:
      syntax: FWD:{dna_bases};REV:{dna_bases}
      interpolated: true
  stranded_orientation:
    name: stranded_orientation
    description: Lists the strand orientiation for a stranded RNA library preparation.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    owner: LibraryPreparation
    domain_of:
    - LibraryPreparation
    range: StrandedOrientationEnum
  target_gene:
    name: target_gene
    description: Targeted gene or locus name for marker gene studies
    title: target gene
    examples:
    - value: 16S rRNA, 18S rRNA, nif, amoA, rpo
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    keywords:
    - target
    slot_uri: MIXS:0000044
    owner: LibraryPreparation
    domain_of:
    - LibraryPreparation
    range: TargetGeneEnum
  target_subfragment:
    name: target_subfragment
    description: Name of subfragment of a gene or locus. Important to e.g. identify
      special regions on marker genes like V6 on 16S rRNA
    title: target subfragment
    examples:
    - value: V6, V9, ITS
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    keywords:
    - target
    slot_uri: MIXS:0000045
    owner: LibraryPreparation
    domain_of:
    - LibraryPreparation
    range: TextValue
  library_selection:
    name: library_selection
    description: Library selection or enrichment method used
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://github.com/enasequence/webin-xml/blob/2.1.0/src/main/resources/uk/ac/ebi/ena/sra/schema/SRA.experiment.xsd
    rank: 1000
    owner: LibraryPreparation
    domain_of:
    - LibraryPreparation
    range: LibrarySelectionEnum
  library_strategy:
    name: library_strategy
    description: Sequencing technique intended for this library
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://github.com/enasequence/webin-xml/blob/2.1.0/src/main/resources/uk/ac/ebi/ena/sra/schema/SRA.experiment.xsd
    rank: 1000
    owner: LibraryPreparation
    domain_of:
    - LibraryPreparation
    range: LibraryStrategyEnum
  library_source:
    name: library_source
    description: The molecular source of the sequencing library
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://github.com/enasequence/webin-xml/blob/2.1.0/src/main/resources/uk/ac/ebi/ena/sra/schema/SRA.experiment.xsd
    rank: 1000
    owner: LibraryPreparation
    domain_of:
    - LibraryPreparation
    range: LibrarySourceEnum
  lib_layout:
    name: lib_layout
    description: Specify whether to expect single, paired, or other configuration
      of reads
    title: library layout
    examples:
    - value: paired
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    keywords:
    - library
    slot_uri: MIXS:0000041
    owner: LibraryPreparation
    domain_of:
    - LibraryPreparation
    range: LibLayoutEnum
  adapters:
    name: adapters
    description: Adapters provide priming sequences for both amplification and sequencing
      of the sample-library fragments. Both adapters should be reported; in uppercase
      letters
    title: adapters
    examples:
    - value: AATGATACGGCGACCACCGAGATCTACACGCT;CAAGCAGAAGACGGCATACGAGAT
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    slot_uri: MIXS:0000048
    owner: LibraryPreparation
    domain_of:
    - LibraryPreparation
    range: string
    structured_pattern:
      syntax: ^{dna_bases};{dna_bases}$
      interpolated: true
      partial_match: true
  instrument_used:
    name: instrument_used
    description: What instrument was used during DataGeneration or MaterialProcessing.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    owner: LibraryPreparation
    domain_of:
    - DataGeneration
    - MaterialProcessing
    range: Instrument
    multivalued: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:inst-{id_shoulder}-{id_blade}$'
      interpolated: true
  has_input:
    name: has_input
    description: An input to a process.
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - input
    rank: 1000
    owner: LibraryPreparation
    domain_of:
    - PlannedProcess
    range: Sample
    required: true
    multivalued: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'
      interpolated: true
  has_output:
    name: has_output
    description: An output from a process.
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - output
    rank: 1000
    owner: LibraryPreparation
    domain_of:
    - PlannedProcess
    range: ProcessedSample
    required: true
    multivalued: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:(procsm)-{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
    owner: LibraryPreparation
    domain_of:
    - PlannedProcess
    range: ProcessingInstitutionEnum
  protocol_link:
    name: protocol_link
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    owner: LibraryPreparation
    domain_of:
    - Configuration
    - 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
    owner: LibraryPreparation
    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
    owner: LibraryPreparation
    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
    owner: LibraryPreparation
    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
    owner: LibraryPreparation
    domain_of:
    - PlannedProcess
    range: string
  has_failure_categorization:
    name: has_failure_categorization
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    owner: LibraryPreparation
    domain_of:
    - PlannedProcess
    range: FailureCategorization
    multivalued: true
    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
    notes:
    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'
    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters
      will be accepted
    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked
      via per-class id slot usage assertions
    - minting authority shoulders should probably be enumerated and checked in the
      pattern
    examples:
    - value: nmdc:mgmag-00-x012.1_7_c1
      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248
    from_schema: https://w3id.org/nmdc/nmdc
    structured_aliases:
    - literal_form: workflow_execution_id
      predicate: NARROW_SYNONYM
      contexts:
      - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml
    - literal_form: data_object_id
      predicate: NARROW_SYNONYM
      contexts:
      - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml
    rank: 1000
    identifier: true
    owner: LibraryPreparation
    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}:libprp-{id_shoulder}-{id_blade}$'
      interpolated: true
  name:
    name: name
    description: A human readable label for an entity
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    owner: LibraryPreparation
    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
    owner: LibraryPreparation
    domain_of:
    - ImageValue
    - NamedThing
    - Protocol
    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
    owner: LibraryPreparation
    domain_of:
    - NamedThing
    - MetaboliteIdentification
    range: uriorcurie
    multivalued: true
    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:
    - 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
    structured_aliases:
    - literal_form: workflow_execution_class
      predicate: NARROW_SYNONYM
      contexts:
      - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml
    rank: 1000
    slot_uri: rdf:type
    designates_type: true
    owner: LibraryPreparation
    domain_of:
    - EukEval
    - FunctionalAnnotationAggMember
    - PeptideQuantification
    - ProteinQuantification
    - GenomeFeature
    - FunctionalAnnotation
    - AttributeValue
    - NamedThing
    - OntologyRelation
    - FailureCategorization
    - Protocol
    - CreditAssociation
    - Doi
    - ProvenanceMetadata
    - MobilePhaseSegment
    - PortionOfSubstance
    - MagBin
    - MetaboliteIdentification
    range: uriorcurie
    required: true
class_uri: nmdc:LibraryPreparation