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Class: SequencingInfo

Information on sequencing info

URI: portable_microhaplotype_object:SequencingInfo

classDiagram class SequencingInfo click SequencingInfo href "../SequencingInfo" SequencingInfo : lib_kit SequencingInfo : lib_layout SequencingInfo : lib_screen 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 SequencingInfo : sequencing_info_id

Slots

Name Cardinality and Range Description Inheritance
sequencing_info_id 1
String		 a unique identifier for this sequencing info direct
seq_instrument 1
String		 the sequencing instrument 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 1
String		 Link to a reference or kit that describes the recovery of nucleic acids from ... direct
nucl_acid_amp 1
String		 Link to a reference or kit that describes the enzymatic amplification of nucl... direct
nucl_acid_ext_date 1
String		 the date of the nucleoacide extraction direct
nucl_acid_amp_date 1
String		 the date of the nucleoacide amplification direct
pcr_cond 1
String		 the method/conditions for PCR, List PCR cycles used to amplify the target direct
lib_screen 1
String		 Describe enrichment, screening, or normalization methods applied during ampli... direct
lib_layout 1
String		 Specify the configuration of reads, e direct
lib_kit 1
String		 Name, version, and applicable cell or cycle numbers for the kit used to prepa... direct
seq_center 1
String		 Name of facility where sequencing was performed (lab, core facility, or compa... direct

Usages

used by used in type used
PortableMicrohaplotypeObject sequencing_infos 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
slots:
- sequencing_info_id
slot_usage:
  sequencing_info_id:
    name: sequencing_info_id
    identifier: true
    domain_of:
    - ExperimentInfo
    - SequencingInfo
attributes:
  seq_instrument:
    name: seq_instrument
    description: the sequencing instrument used to sequence the run, e.g. ILLUMINA,
      Illumina MiSeq
    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
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - SequencingInfo
    range: string
    required: true
    pattern: r"\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
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - SequencingInfo
    range: string
    required: true
    pattern: r"^(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,
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - SequencingInfo
    range: string
    required: true
    pattern: r"^(https?|ftp):\/\/[^\s/$.?#].[^\s]*$"
  nucl_acid_ext_date:
    name: nucl_acid_ext_date
    description: the date of the nucleoacide extraction
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - SequencingInfo
    range: string
    required: true
    pattern: r"\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 nucleoacide amplification
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - SequencingInfo
    range: string
    required: true
    pattern: r"\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: true
    pattern: ^[A-z-._0-9 ]$
  lib_screen:
    name: lib_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
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - SequencingInfo
    range: string
    required: true
    pattern: ^[A-z-._0-9 ]$
  lib_layout:
    name: lib_layout
    description: Specify the configuration of reads, e.g. paired-end
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - SequencingInfo
    range: string
    required: true
    pattern: ^[A-z-._0-9 ]$
  lib_kit:
    name: lib_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
    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)
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - SequencingInfo
    range: string
    required: true
    pattern: ^[A-z-._0-9 ]$

Induced

name: SequencingInfo
description: Information on sequencing info
from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
slot_usage:
  sequencing_info_id:
    name: sequencing_info_id
    identifier: true
    domain_of:
    - ExperimentInfo
    - SequencingInfo
attributes:
  seq_instrument:
    name: seq_instrument
    description: the sequencing instrument used to sequence the run, e.g. ILLUMINA,
      Illumina MiSeq
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: seq_instrument
    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
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: seq_date
    owner: SequencingInfo
    domain_of:
    - SequencingInfo
    range: string
    required: true
    pattern: r"\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
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: nucl_acid_ext
    owner: SequencingInfo
    domain_of:
    - SequencingInfo
    range: string
    required: true
    pattern: r"^(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,
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: nucl_acid_amp
    owner: SequencingInfo
    domain_of:
    - SequencingInfo
    range: string
    required: true
    pattern: r"^(https?|ftp):\/\/[^\s/$.?#].[^\s]*$"
  nucl_acid_ext_date:
    name: nucl_acid_ext_date
    description: the date of the nucleoacide extraction
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: nucl_acid_ext_date
    owner: SequencingInfo
    domain_of:
    - SequencingInfo
    range: string
    required: true
    pattern: r"\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 nucleoacide amplification
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: nucl_acid_amp_date
    owner: SequencingInfo
    domain_of:
    - SequencingInfo
    range: string
    required: true
    pattern: r"\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: true
    pattern: ^[A-z-._0-9 ]$
  lib_screen:
    name: lib_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
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: lib_screen
    owner: SequencingInfo
    domain_of:
    - SequencingInfo
    range: string
    required: true
    pattern: ^[A-z-._0-9 ]$
  lib_layout:
    name: lib_layout
    description: Specify the configuration of reads, e.g. paired-end
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: lib_layout
    owner: SequencingInfo
    domain_of:
    - SequencingInfo
    range: string
    required: true
    pattern: ^[A-z-._0-9 ]$
  lib_kit:
    name: lib_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
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: lib_kit
    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)
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: seq_center
    owner: SequencingInfo
    domain_of:
    - SequencingInfo
    range: string
    required: true
    pattern: ^[A-z-._0-9 ]$
  sequencing_info_id:
    name: sequencing_info_id
    description: a unique identifier for this sequencing info
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    identifier: true
    alias: sequencing_info_id
    owner: SequencingInfo
    domain_of:
    - ExperimentInfo
    - SequencingInfo
    range: string
    required: true
    pattern: ^[A-z-._0-9 ]$