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Class: ExperimentNanopore

Table containing experiment_nanopore information

URI: gregor_linkml:ExperimentNanopore

classDiagram class ExperimentNanopore click ExperimentNanopore href "../ExperimentNanopore" ExperimentNanopore : analyte_id ExperimentNanopore : barcode_kit ExperimentNanopore : chemistry_type ExperimentNanopore --> "0..1" ChemistryTypeEnum : chemistry_type click ChemistryTypeEnum href "../ChemistryTypeEnum" ExperimentNanopore : date_data_generation ExperimentNanopore : experiment_nanopore_id ExperimentNanopore : experiment_sample_id ExperimentNanopore : experiment_type ExperimentNanopore --> "1" ExperimentTypeEnum : experiment_type click ExperimentTypeEnum href "../ExperimentTypeEnum" ExperimentNanopore : fragmentation_method ExperimentNanopore : seq_library_prep_kit_method ExperimentNanopore : sequencing_platform ExperimentNanopore : targeted_region_bed_file ExperimentNanopore : targeted_regions_method ExperimentNanopore : was_barcoded

Slots

Name Cardinality and Range Description Inheritance
experiment_nanopore_id 1
String		 identifier for experiment direct
analyte_id 1
String		 direct
experiment_sample_id 0..1
String		 identifier used in the data file (e direct
seq_library_prep_kit_method 0..1
String		 Library prep kit used direct
fragmentation_method 0..1
String		 method used for shearing/fragmentation direct
experiment_type 1
ExperimentTypeEnum		 direct
targeted_regions_method 0..1
String		 Which capture kit is used direct
targeted_region_bed_file 0..1
String		 name and path of bed file uploaded to workspace direct
date_data_generation 0..1
Date		 Date of data generation (First sequencing date) direct
sequencing_platform 0..1
String		 sequencing platform used for the experiment direct
chemistry_type 0..1
ChemistryTypeEnum		 chemistry type used for the experiment direct
was_barcoded 1
Boolean		 indicates whether samples were barcoded on this flowcell direct
barcode_kit 0..1
String		 Barcode kit used direct

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/madanucd/gregor_linkml

Mappings

Mapping Type Mapped Value
self gregor_linkml:ExperimentNanopore
native gregor_linkml:ExperimentNanopore

LinkML Source

Direct

name: Experiment_nanopore
description: Table containing experiment_nanopore information
from_schema: https://w3id.org/madanucd/gregor_linkml
slots:
- experiment_nanopore_id
- analyte_id
- experiment_sample_id
- seq_library_prep_kit_method
- fragmentation_method
- experiment_type
- targeted_regions_method
- targeted_region_bed_file
- date_data_generation
- sequencing_platform
- chemistry_type
- was_barcoded
- barcode_kit

Induced

name: Experiment_nanopore
description: Table containing experiment_nanopore information
from_schema: https://w3id.org/madanucd/gregor_linkml
attributes:
  experiment_nanopore_id:
    name: experiment_nanopore_id
    description: identifier for experiment
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: experiment_nanopore_id
    owner: Experiment_nanopore
    domain_of:
    - Experiment_nanopore
    - Aligned_nanopore
    range: string
    required: true
  analyte_id:
    name: analyte_id
    description: ''
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: analyte_id
    owner: Experiment_nanopore
    domain_of:
    - Analyte
    - Experiment_dna_short_read
    - Experiment_rna_short_read
    - Experiment_nanopore
    - Experiment_pac_bio
    - Experiment_atac_short_read
    range: string
    required: true
  experiment_sample_id:
    name: experiment_sample_id
    description: identifier used in the data file (e.g. the SM tag in a BAM header,
      column headers for genotype fields in a VCF file)
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: experiment_sample_id
    owner: Experiment_nanopore
    domain_of:
    - Experiment_dna_short_read
    - Experiment_rna_short_read
    - Experiment_nanopore
    - Experiment_pac_bio
    - Experiment_atac_short_read
    range: string
  seq_library_prep_kit_method:
    name: seq_library_prep_kit_method
    description: Library prep kit used
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: seq_library_prep_kit_method
    owner: Experiment_nanopore
    domain_of:
    - Experiment_dna_short_read
    - Experiment_rna_short_read
    - Experiment_nanopore
    - Experiment_pac_bio
    - Experiment_atac_short_read
    range: string
  fragmentation_method:
    name: fragmentation_method
    description: method used for shearing/fragmentation
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: fragmentation_method
    owner: Experiment_nanopore
    domain_of:
    - Experiment_nanopore
    - Experiment_pac_bio
    range: string
  experiment_type:
    name: experiment_type
    description: ''
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: experiment_type
    owner: Experiment_nanopore
    domain_of:
    - Experiment_dna_short_read
    - Experiment_rna_short_read
    - Experiment_nanopore
    - Experiment_pac_bio
    - Experiment_atac_short_read
    range: Experiment_typeEnum
    required: true
  targeted_regions_method:
    name: targeted_regions_method
    description: Which capture kit is used. Can be missing if RC receives external
      data
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: targeted_regions_method
    owner: Experiment_nanopore
    domain_of:
    - Experiment_dna_short_read
    - Experiment_nanopore
    - Experiment_pac_bio
    - Experiment_atac_short_read
    range: string
  targeted_region_bed_file:
    name: targeted_region_bed_file
    description: name and path of bed file uploaded to workspace
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: targeted_region_bed_file
    owner: Experiment_nanopore
    domain_of:
    - Experiment_dna_short_read
    - Experiment_nanopore
    - Experiment_pac_bio
    - Experiment_atac_short_read
    range: string
  date_data_generation:
    name: date_data_generation
    description: Date of data generation (First sequencing date)
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: date_data_generation
    owner: Experiment_nanopore
    domain_of:
    - Experiment_dna_short_read
    - Experiment_rna_short_read
    - Experiment_nanopore
    - Experiment_pac_bio
    - Experiment_atac_short_read
    range: date
  sequencing_platform:
    name: sequencing_platform
    description: sequencing platform used for the experiment
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: sequencing_platform
    owner: Experiment_nanopore
    domain_of:
    - Experiment_dna_short_read
    - Experiment_rna_short_read
    - Experiment_nanopore
    - Experiment_pac_bio
    - Experiment_atac_short_read
    range: string
  chemistry_type:
    name: chemistry_type
    description: chemistry type used for the experiment
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: chemistry_type
    owner: Experiment_nanopore
    domain_of:
    - Experiment_nanopore
    range: Chemistry_typeEnum
  was_barcoded:
    name: was_barcoded
    description: indicates whether samples were barcoded on this flowcell
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: was_barcoded
    owner: Experiment_nanopore
    domain_of:
    - Experiment_nanopore
    - Experiment_pac_bio
    range: boolean
    required: true
  barcode_kit:
    name: barcode_kit
    description: Barcode kit used
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: barcode_kit
    owner: Experiment_nanopore
    domain_of:
    - Experiment_nanopore
    - Experiment_pac_bio
    range: string