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Class: SequencingInfo

Information on sequencing info

URI: portable_microhaplotype_object:SequencingInfo

classDiagram class SequencingInfo click SequencingInfo href "../SequencingInfo" SequencingInfo : library_kit SequencingInfo : library_layout SequencingInfo : library_screen SequencingInfo : library_selection SequencingInfo : library_source SequencingInfo : library_strategy SequencingInfo : nucl_acid_amp SequencingInfo : nucl_acid_amp_date SequencingInfo : nucl_acid_ext SequencingInfo : nucl_acid_ext_date SequencingInfo : pcr_cond SequencingInfo : seq_center SequencingInfo : seq_date SequencingInfo : seq_instrument_model SequencingInfo : seq_platform SequencingInfo : sequencing_info_name

Slots

Name Cardinality and Range Description Inheritance
sequencing_info_name 1
String		 a name of for the sequencing done, e direct
seq_platform 1
String		 the sequencing technology used to sequence the run, e direct
seq_instrument_model 1
String		 the sequencing instrument model used to sequence the run, e direct
seq_date 1
String		 the date of sequencing, should be YYYY-MM or YYYY-MM-DD direct
nucl_acid_ext 0..1
String		 Link to a reference or kit that describes the recovery of nucleic acids from ... direct
nucl_acid_amp 0..1
String		 Link to a reference or kit that describes the enzymatic amplification of nucl... direct
nucl_acid_ext_date 0..1
String		 the date of the nucleoacid extraction direct
nucl_acid_amp_date 0..1
String		 the date of the nucleoacid amplification direct
pcr_cond 0..1
String		 the method/conditions for PCR, List PCR cycles used to amplify the target direct
library_screen 0..1
String		 Describe enrichment, screening, or normalization methods applied during ampli... direct
library_kit 0..1
String		 Name, version, and applicable cell or cycle numbers for the kit used to prepa... direct
library_layout 1
String		 Specify the configuration of reads, e direct
library_strategy 1
String		 what the nuceloacid sequencing/amplification strategy was (common names are A... direct
library_source 1
String		 Source of amplification material (common names GENOMIC, TRANSCRIPTOMIC) direct
library_selection 1
String		 how amplification was done (common are PCR=Source material was selected by de... direct
seq_center 0..1
String		 Name of facility where sequencing was performed (lab, core facility, or compa... direct

Usages

used by used in type used
PortableMicrohaplotypeObject sequencing_info range SequencingInfo

Identifier and Mapping Information

Schema Source

  • from schema: https://plasmogenepi.github.io/portable-microhaplotype-object

Mappings

Mapping Type Mapped Value
self portable_microhaplotype_object:SequencingInfo
native portable_microhaplotype_object:SequencingInfo

LinkML Source

Direct

name: SequencingInfo
description: Information on sequencing info
from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
attributes:
  sequencing_info_name:
    name: sequencing_info_name
    description: a name of for the sequencing done, e.g. batch1
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - SequencingInfo
    range: string
    required: true
    pattern: ^[A-z-._0-9 ]+$
  seq_platform:
    name: seq_platform
    description: the sequencing technology used to sequence the run, e.g. ILLUMINA,
      NANOPORE, PACBIO
    examples:
    - value: ILLUMINA
    - value: PACBIO
    - value: NANOPORE
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - SequencingInfo
    range: string
    required: true
    pattern: ^[A-z-._0-9 ]+$
  seq_instrument_model:
    name: seq_instrument_model
    description: the sequencing instrument model used to sequence the run, e.g. NextSeq
      2000, MinION, Revio
    examples:
    - value: NextSeq 2000
    - value: MinION
    - value: Revio
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - SequencingInfo
    range: string
    required: true
    pattern: ^[A-z-._0-9 ]+$
  seq_date:
    name: seq_date
    description: the date of sequencing, should be YYYY-MM or YYYY-MM-DD
    examples:
    - value: '2024-03-10'
    - value: 2024-03
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - SequencingInfo
    range: string
    required: true
    pattern: \d{4}-(?:0[1-9]|1[0-2])(?:-(?:0[1-9]|[12][0-9]|3[01]))?
  nucl_acid_ext:
    name: nucl_acid_ext
    description: Link to a reference or kit that describes the recovery of nucleic
      acids from the sample
    examples:
    - value: https://www.paragongenomics.com/targeted-sequencing/amplicon-sequencing/cleanplex-ngs-amplicon-sequencing/
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - SequencingInfo
    range: string
    required: false
    pattern: ^(https?|ftp):\/\/[^\s/$.?#].[^\s]*$
  nucl_acid_amp:
    name: nucl_acid_amp
    description: Link to a reference or kit that describes the enzymatic amplification
      of nucleic acids
    examples:
    - value: https://www.paragongenomics.com/targeted-sequencing/amplicon-sequencing/cleanplex-ngs-amplicon-sequencing/
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - SequencingInfo
    range: string
    required: false
    pattern: ^(https?|ftp):\/\/[^\s/$.?#].[^\s]*$
  nucl_acid_ext_date:
    name: nucl_acid_ext_date
    description: the date of the nucleoacid extraction
    examples:
    - value: '2024-03-10'
    - value: 2024-03
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - SequencingInfo
    range: string
    required: false
    pattern: \d{4}-(?:0[1-9]|1[0-2])(?:-(?:0[1-9]|[12][0-9]|3[01]))?
  nucl_acid_amp_date:
    name: nucl_acid_amp_date
    description: the date of the nucleoacid amplification
    examples:
    - value: '2024-03-10'
    - value: 2024-03
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - SequencingInfo
    range: string
    required: false
    pattern: \d{4}-(?:0[1-9]|1[0-2])(?:-(?:0[1-9]|[12][0-9]|3[01]))?
  pcr_cond:
    name: pcr_cond
    description: the method/conditions for PCR, List PCR cycles used to amplify the
      target
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - SequencingInfo
    range: string
    required: false
    pattern: ^[A-z-._0-9\(\),\/\ ]+$
  library_screen:
    name: library_screen
    description: Describe enrichment, screening, or normalization methods applied
      during amplification or library preparation, e.g. size selection 390bp, diluted
      to 1 ng DNA/sample
    examples:
    - value: size selection 390bp, diluted to 1 ng DNA/sample
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - SequencingInfo
    range: string
    required: false
    pattern: ^[A-z-._0-9\(\),\/\ ]+$
  library_kit:
    name: library_kit
    description: Name, version, and applicable cell or cycle numbers for the kit used
      to prepare libraries and load cells or chips for sequencing. If possible, include
      a part number, e.g. MiSeq Reagent Kit v3 (150-cycle), MS-102-3001
    examples:
    - value: MiSeq Reagent Kit v3 (150-cycle), MS-102-3001
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - SequencingInfo
    range: string
    required: false
    pattern: ^[A-z-._0-9\(\),\/\ ]+$
  library_layout:
    name: library_layout
    description: Specify the configuration of reads, e.g. paired-end, single
    examples:
    - value: paired-end
    - value: single
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - SequencingInfo
    range: string
    required: true
    pattern: ^[A-z-._0-9 ]+$
  library_strategy:
    name: library_strategy
    description: what the nuceloacid sequencing/amplification strategy was (common
      names are AMPLICON, WGS)
    examples:
    - value: AMPLICON
    - value: WGS
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - SequencingInfo
    range: string
    required: true
    pattern: ^[A-z-._0-9 ]+$
  library_source:
    name: library_source
    description: Source of amplification material (common names GENOMIC, TRANSCRIPTOMIC)
    examples:
    - value: GENOMIC
    - value: TRANSCRIPTOMIC
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - SequencingInfo
    range: string
    required: true
    pattern: ^[A-z-._0-9 ]+$
  library_selection:
    name: library_selection
    description: how amplification was done (common are PCR=Source material was selected
      by designed primers, RANDOM =Random selection by shearing or other method)
    examples:
    - value: PCR
    - value: RANDOM
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - SequencingInfo
    range: string
    required: true
    pattern: ^[A-z-._0-9 ]+$
  seq_center:
    name: seq_center
    description: Name of facility where sequencing was performed (lab, core facility,
      or company)
    examples:
    - value: UCSF sequencing core
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - SequencingInfo
    range: string
    required: false
    pattern: ^[A-z-._0-9\(\),\/\ ]+$

Induced

name: SequencingInfo
description: Information on sequencing info
from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
attributes:
  sequencing_info_name:
    name: sequencing_info_name
    description: a name of for the sequencing done, e.g. batch1
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: sequencing_info_name
    owner: SequencingInfo
    domain_of:
    - SequencingInfo
    range: string
    required: true
    pattern: ^[A-z-._0-9 ]+$
  seq_platform:
    name: seq_platform
    description: the sequencing technology used to sequence the run, e.g. ILLUMINA,
      NANOPORE, PACBIO
    examples:
    - value: ILLUMINA
    - value: PACBIO
    - value: NANOPORE
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: seq_platform
    owner: SequencingInfo
    domain_of:
    - SequencingInfo
    range: string
    required: true
    pattern: ^[A-z-._0-9 ]+$
  seq_instrument_model:
    name: seq_instrument_model
    description: the sequencing instrument model used to sequence the run, e.g. NextSeq
      2000, MinION, Revio
    examples:
    - value: NextSeq 2000
    - value: MinION
    - value: Revio
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: seq_instrument_model
    owner: SequencingInfo
    domain_of:
    - SequencingInfo
    range: string
    required: true
    pattern: ^[A-z-._0-9 ]+$
  seq_date:
    name: seq_date
    description: the date of sequencing, should be YYYY-MM or YYYY-MM-DD
    examples:
    - value: '2024-03-10'
    - value: 2024-03
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: seq_date
    owner: SequencingInfo
    domain_of:
    - SequencingInfo
    range: string
    required: true
    pattern: \d{4}-(?:0[1-9]|1[0-2])(?:-(?:0[1-9]|[12][0-9]|3[01]))?
  nucl_acid_ext:
    name: nucl_acid_ext
    description: Link to a reference or kit that describes the recovery of nucleic
      acids from the sample
    examples:
    - value: https://www.paragongenomics.com/targeted-sequencing/amplicon-sequencing/cleanplex-ngs-amplicon-sequencing/
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: nucl_acid_ext
    owner: SequencingInfo
    domain_of:
    - SequencingInfo
    range: string
    required: false
    pattern: ^(https?|ftp):\/\/[^\s/$.?#].[^\s]*$
  nucl_acid_amp:
    name: nucl_acid_amp
    description: Link to a reference or kit that describes the enzymatic amplification
      of nucleic acids
    examples:
    - value: https://www.paragongenomics.com/targeted-sequencing/amplicon-sequencing/cleanplex-ngs-amplicon-sequencing/
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: nucl_acid_amp
    owner: SequencingInfo
    domain_of:
    - SequencingInfo
    range: string
    required: false
    pattern: ^(https?|ftp):\/\/[^\s/$.?#].[^\s]*$
  nucl_acid_ext_date:
    name: nucl_acid_ext_date
    description: the date of the nucleoacid extraction
    examples:
    - value: '2024-03-10'
    - value: 2024-03
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: nucl_acid_ext_date
    owner: SequencingInfo
    domain_of:
    - SequencingInfo
    range: string
    required: false
    pattern: \d{4}-(?:0[1-9]|1[0-2])(?:-(?:0[1-9]|[12][0-9]|3[01]))?
  nucl_acid_amp_date:
    name: nucl_acid_amp_date
    description: the date of the nucleoacid amplification
    examples:
    - value: '2024-03-10'
    - value: 2024-03
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: nucl_acid_amp_date
    owner: SequencingInfo
    domain_of:
    - SequencingInfo
    range: string
    required: false
    pattern: \d{4}-(?:0[1-9]|1[0-2])(?:-(?:0[1-9]|[12][0-9]|3[01]))?
  pcr_cond:
    name: pcr_cond
    description: the method/conditions for PCR, List PCR cycles used to amplify the
      target
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: pcr_cond
    owner: SequencingInfo
    domain_of:
    - SequencingInfo
    range: string
    required: false
    pattern: ^[A-z-._0-9\(\),\/\ ]+$
  library_screen:
    name: library_screen
    description: Describe enrichment, screening, or normalization methods applied
      during amplification or library preparation, e.g. size selection 390bp, diluted
      to 1 ng DNA/sample
    examples:
    - value: size selection 390bp, diluted to 1 ng DNA/sample
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: library_screen
    owner: SequencingInfo
    domain_of:
    - SequencingInfo
    range: string
    required: false
    pattern: ^[A-z-._0-9\(\),\/\ ]+$
  library_kit:
    name: library_kit
    description: Name, version, and applicable cell or cycle numbers for the kit used
      to prepare libraries and load cells or chips for sequencing. If possible, include
      a part number, e.g. MiSeq Reagent Kit v3 (150-cycle), MS-102-3001
    examples:
    - value: MiSeq Reagent Kit v3 (150-cycle), MS-102-3001
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: library_kit
    owner: SequencingInfo
    domain_of:
    - SequencingInfo
    range: string
    required: false
    pattern: ^[A-z-._0-9\(\),\/\ ]+$
  library_layout:
    name: library_layout
    description: Specify the configuration of reads, e.g. paired-end, single
    examples:
    - value: paired-end
    - value: single
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: library_layout
    owner: SequencingInfo
    domain_of:
    - SequencingInfo
    range: string
    required: true
    pattern: ^[A-z-._0-9 ]+$
  library_strategy:
    name: library_strategy
    description: what the nuceloacid sequencing/amplification strategy was (common
      names are AMPLICON, WGS)
    examples:
    - value: AMPLICON
    - value: WGS
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: library_strategy
    owner: SequencingInfo
    domain_of:
    - SequencingInfo
    range: string
    required: true
    pattern: ^[A-z-._0-9 ]+$
  library_source:
    name: library_source
    description: Source of amplification material (common names GENOMIC, TRANSCRIPTOMIC)
    examples:
    - value: GENOMIC
    - value: TRANSCRIPTOMIC
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: library_source
    owner: SequencingInfo
    domain_of:
    - SequencingInfo
    range: string
    required: true
    pattern: ^[A-z-._0-9 ]+$
  library_selection:
    name: library_selection
    description: how amplification was done (common are PCR=Source material was selected
      by designed primers, RANDOM =Random selection by shearing or other method)
    examples:
    - value: PCR
    - value: RANDOM
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: library_selection
    owner: SequencingInfo
    domain_of:
    - SequencingInfo
    range: string
    required: true
    pattern: ^[A-z-._0-9 ]+$
  seq_center:
    name: seq_center
    description: Name of facility where sequencing was performed (lab, core facility,
      or company)
    examples:
    - value: UCSF sequencing core
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: seq_center
    owner: SequencingInfo
    domain_of:
    - SequencingInfo
    range: string
    required: false
    pattern: ^[A-z-._0-9\(\),\/\ ]+$