Class: ExperimentDnaShortRead

Table containing experiment_dna_short_read information

URI: gregor_linkml:ExperimentDnaShortRead

classDiagram class ExperimentDnaShortRead click ExperimentDnaShortRead href "../ExperimentDnaShortRead" ExperimentDnaShortRead : analyte_id ExperimentDnaShortRead : date_data_generation ExperimentDnaShortRead : experiment_dna_short_read_id ExperimentDnaShortRead : experiment_sample_id ExperimentDnaShortRead : experiment_type ExperimentDnaShortRead --> "1" ExperimentTypeEnum : experiment_type click ExperimentTypeEnum href "../ExperimentTypeEnum" ExperimentDnaShortRead : read_length ExperimentDnaShortRead : seq_library_prep_kit_method ExperimentDnaShortRead : sequencing_event_details ExperimentDnaShortRead : sequencing_platform ExperimentDnaShortRead : target_insert_size ExperimentDnaShortRead : targeted_region_bed_file ExperimentDnaShortRead : targeted_regions_method

Slots

Name	Cardinality and Range	Description	Inheritance
experiment_dna_short_read_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
read_length	0..1 Integer	sequenced read length (bp); GREGoR RCs do paired end sequencing, so is the ex...	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
target_insert_size	0..1 Integer	insert size the protocol targets for DNA fragments	direct
sequencing_platform	0..1 String	sequencing platform used for the experiment	direct
sequencing_event_details	0..1 String	describe if there are any sequencing-specific issues that would be important ...	direct

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Experiment_dna_short_read
description: Table containing experiment_dna_short_read information
from_schema: https://w3id.org/madanucd/gregor_linkml
slots:
- experiment_dna_short_read_id
- analyte_id
- experiment_sample_id
- seq_library_prep_kit_method
- read_length
- experiment_type
- targeted_regions_method
- targeted_region_bed_file
- date_data_generation
- target_insert_size
- sequencing_platform
- sequencing_event_details

Induced

name: Experiment_dna_short_read
description: Table containing experiment_dna_short_read information
from_schema: https://w3id.org/madanucd/gregor_linkml
attributes:
  experiment_dna_short_read_id:
    name: experiment_dna_short_read_id
    description: identifier for experiment
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: experiment_dna_short_read_id
    owner: Experiment_dna_short_read
    domain_of:
    - Experiment_dna_short_read
    - Aligned_dna_short_read
    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_dna_short_read
    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_dna_short_read
    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_dna_short_read
    domain_of:
    - Experiment_dna_short_read
    - Experiment_rna_short_read
    - Experiment_nanopore
    - Experiment_pac_bio
    - Experiment_atac_short_read
    range: string
  read_length:
    name: read_length
    description: sequenced read length (bp); GREGoR RCs do paired end sequencing,
      so is the example of 100bp indicates 2x100bp.
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: read_length
    owner: Experiment_dna_short_read
    domain_of:
    - Experiment_dna_short_read
    - Experiment_rna_short_read
    - Experiment_atac_short_read
    range: integer
  experiment_type:
    name: experiment_type
    description: ''
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: experiment_type
    owner: Experiment_dna_short_read
    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_dna_short_read
    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_dna_short_read
    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_dna_short_read
    domain_of:
    - Experiment_dna_short_read
    - Experiment_rna_short_read
    - Experiment_nanopore
    - Experiment_pac_bio
    - Experiment_atac_short_read
    range: date
  target_insert_size:
    name: target_insert_size
    description: insert size the protocol targets for DNA fragments
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: target_insert_size
    owner: Experiment_dna_short_read
    domain_of:
    - Experiment_dna_short_read
    - Experiment_atac_short_read
    range: integer
  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_dna_short_read
    domain_of:
    - Experiment_dna_short_read
    - Experiment_rna_short_read
    - Experiment_nanopore
    - Experiment_pac_bio
    - Experiment_atac_short_read
    range: string
  sequencing_event_details:
    name: sequencing_event_details
    description: describe if there are any sequencing-specific issues that would be
      important to note
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: sequencing_event_details
    owner: Experiment_dna_short_read
    domain_of:
    - Experiment_dna_short_read
    range: string