Class: Sequencing Run (SequencingRun)

A record of a sequencing experiment, including run metadata and output data files.

 classDiagram
    class SequencingRun
    click SequencingRun href "../SequencingRun/"
      SequencingRun : sequencing_batch_number

      SequencingRun : sequencing_facility

      SequencingRun : sequencing_kit

      SequencingRun : sequencing_platform

      SequencingRun : sequencing_run_date

      SequencingRun : total_reads_passing_qc_filter

Slots

Name	Cardinality and Range	Description	Inheritance
sequencing_batch_number	0..1 recommended String	ID of sequencing run assigned by the sequencing facility	direct
total_reads_passing_qc_filter	0..1 recommended Integer	Number of usable reads for analysis	direct
sequencing_platform	0..1 recommended String	Designation of sequencing instrument used	direct
sequencing_facility	0..1 recommended String	Name and address of sequencing facility	direct
sequencing_run_date	0..1 recommended Date	Date of sequencing run in the format year-month-day	direct
sequencing_kit	0..1 recommended String	Name, manufacturer, order and lot numbers of sequencing kit	direct

Usages

used by	used in	type	used
AIRRRun	sequencing_run	range	SequencingRun

Identifier and Mapping Information

Schema Source

from schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema

Mappings

Mapping Type	Mapped Value
self	nfdi4immuno:SequencingRun
native	nfdi4immuno:SequencingRun

LinkML Source

Direct

name: SequencingRun
description: A record of a sequencing experiment, including run metadata and output
  data files.
title: Sequencing Run
from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
slots:
- sequencing_batch_number
- total_reads_passing_qc_filter
- sequencing_platform
- sequencing_facility
- sequencing_run_date
- sequencing_kit

Induced

name: SequencingRun
description: A record of a sequencing experiment, including run metadata and output
  data files.
title: Sequencing Run
from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
attributes:
  sequencing_batch_number:
    name: sequencing_batch_number
    description: ID of sequencing run assigned by the sequencing facility.
    title: Batch number
    examples:
    - value: 160101_M01234
    from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
    rank: 1000
    alias: sequencing_batch_number
    owner: SequencingRun
    domain_of:
    - SequencingRun
    range: string
    recommended: true
  total_reads_passing_qc_filter:
    name: total_reads_passing_qc_filter
    description: Number of usable reads for analysis.
    title: Total reads passing QC filter
    examples:
    - value: '10365118'
    from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
    rank: 1000
    alias: total_reads_passing_qc_filter
    owner: SequencingRun
    domain_of:
    - SequencingRun
    range: integer
    recommended: true
  sequencing_platform:
    name: sequencing_platform
    description: Designation of sequencing instrument used.
    title: Sequencing platform
    examples:
    - value: Alumina LoSeq 1000
    from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
    rank: 1000
    alias: sequencing_platform
    owner: SequencingRun
    domain_of:
    - SequencingRun
    range: string
    recommended: true
  sequencing_facility:
    name: sequencing_facility
    description: Name and address of sequencing facility.
    title: Sequencing facility
    examples:
    - value: Seqs-R-Us, Vancouver, BC, Canada
    from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
    rank: 1000
    alias: sequencing_facility
    owner: SequencingRun
    domain_of:
    - SequencingRun
    range: string
    recommended: true
  sequencing_run_date:
    name: sequencing_run_date
    description: Date of sequencing run in the format year-month-day.
    title: Date of sequencing run
    examples:
    - value: '2016-12-16'
    from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
    rank: 1000
    alias: sequencing_run_date
    owner: SequencingRun
    domain_of:
    - SequencingRun
    range: date
    recommended: true
  sequencing_kit:
    name: sequencing_kit
    description: Name, manufacturer, order and lot numbers of sequencing kit.
    title: Sequencing kit
    examples:
    - value: 'FullSeq 600, Alumina, #M123456C0, 789G1HK'
    from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
    rank: 1000
    alias: sequencing_kit
    owner: SequencingRun
    domain_of:
    - SequencingRun
    range: string
    recommended: true