Class: AlignedDnaShortRead

Table containing aligned_dna_short_read information

classDiagram class AlignedDnaShortRead click AlignedDnaShortRead href "../AlignedDnaShortRead" AlignedDnaShortRead : aligned_dna_short_read_file AlignedDnaShortRead : aligned_dna_short_read_id AlignedDnaShortRead : aligned_dna_short_read_index_file AlignedDnaShortRead : alignment_software AlignedDnaShortRead : analysis_details AlignedDnaShortRead : experiment_dna_short_read_id AlignedDnaShortRead : md5sum AlignedDnaShortRead : mean_coverage AlignedDnaShortRead : quality_issues AlignedDnaShortRead : reference_assembly AlignedDnaShortRead --> "1" ReferenceAssemblyEnum : reference_assembly click ReferenceAssemblyEnum href "../ReferenceAssemblyEnum" AlignedDnaShortRead : reference_assembly_details AlignedDnaShortRead : reference_assembly_uri

Slots

Name	Cardinality and Range	Description	Inheritance
aligned_dna_short_read_id	1 String		direct
experiment_dna_short_read_id	1 String	identifier for experiment	direct
aligned_dna_short_read_file	1 String	name and path of file with aligned reads	direct
aligned_dna_short_read_index_file	1 String	name and path of index file corresponding to aligned reads file	direct
md5sum	1 String	md5 checksum for file	direct
reference_assembly	1 ReferenceAssemblyEnum		direct
reference_assembly_uri	0..1 String		direct
reference_assembly_details	0..1 String		direct
alignment_software	1 String	Software including version number	direct
mean_coverage	0..1 Float	Mean coverage of either the genome or the targeted regions	direct
analysis_details	0..1 String	brief description of the analysis pipeline used for producing the asc_file; p...	direct
quality_issues	0..1 String	describe if there are any QC issues that would be important to note	direct

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Aligned_dna_short_read
description: Table containing aligned_dna_short_read information
from_schema: https://w3id.org/madanucd/gregor_linkml
slots:
- aligned_dna_short_read_id
- experiment_dna_short_read_id
- aligned_dna_short_read_file
- aligned_dna_short_read_index_file
- md5sum
- reference_assembly
- reference_assembly_uri
- reference_assembly_details
- alignment_software
- mean_coverage
- analysis_details
- quality_issues

Induced

name: Aligned_dna_short_read
description: Table containing aligned_dna_short_read information
from_schema: https://w3id.org/madanucd/gregor_linkml
attributes:
  aligned_dna_short_read_id:
    name: aligned_dna_short_read_id
    description: ''
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: aligned_dna_short_read_id
    owner: Aligned_dna_short_read
    domain_of:
    - Aligned_dna_short_read
    - Aligned_dna_short_read_set
    range: string
    required: true
  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: Aligned_dna_short_read
    domain_of:
    - Experiment_dna_short_read
    - Aligned_dna_short_read
    range: string
    required: true
  aligned_dna_short_read_file:
    name: aligned_dna_short_read_file
    description: name and path of file with aligned reads
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: aligned_dna_short_read_file
    owner: Aligned_dna_short_read
    domain_of:
    - Aligned_dna_short_read
    range: string
    required: true
  aligned_dna_short_read_index_file:
    name: aligned_dna_short_read_index_file
    description: name and path of index file corresponding to aligned reads file
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: aligned_dna_short_read_index_file
    owner: Aligned_dna_short_read
    domain_of:
    - Aligned_dna_short_read
    range: string
    required: true
  md5sum:
    name: md5sum
    description: md5 checksum for file
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: md5sum
    owner: Aligned_dna_short_read
    domain_of:
    - Aligned_dna_short_read
    - Called_variants_dna_short_read
    - Aligned_rna_short_read
    - Aligned_nanopore
    - Called_variants_nanopore
    - Aligned_pac_bio
    - Called_variants_pac_bio
    - Aligned_atac_short_read
    range: string
    required: true
  reference_assembly:
    name: reference_assembly
    description: ''
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: reference_assembly
    owner: Aligned_dna_short_read
    domain_of:
    - Aligned_dna_short_read
    - Aligned_rna_short_read
    - Aligned_nanopore
    - Aligned_pac_bio
    - Aligned_atac_short_read
    range: Reference_assemblyEnum
    required: true
  reference_assembly_uri:
    name: reference_assembly_uri
    description: ''
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: reference_assembly_uri
    owner: Aligned_dna_short_read
    domain_of:
    - Aligned_dna_short_read
    - Aligned_rna_short_read
    - Aligned_atac_short_read
    range: string
  reference_assembly_details:
    name: reference_assembly_details
    description: ''
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: reference_assembly_details
    owner: Aligned_dna_short_read
    domain_of:
    - Aligned_dna_short_read
    - Aligned_rna_short_read
    - Aligned_atac_short_read
    range: string
  alignment_software:
    name: alignment_software
    description: Software including version number
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: alignment_software
    owner: Aligned_dna_short_read
    domain_of:
    - Aligned_dna_short_read
    - Aligned_rna_short_read
    - Aligned_nanopore
    - Aligned_pac_bio
    - Aligned_atac_short_read
    range: string
    required: true
  mean_coverage:
    name: mean_coverage
    description: Mean coverage of either the genome or the targeted regions
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: mean_coverage
    owner: Aligned_dna_short_read
    domain_of:
    - Aligned_dna_short_read
    - Aligned_rna_short_read
    - Aligned_nanopore
    - Aligned_pac_bio
    - Aligned_atac_short_read
    range: float
  analysis_details:
    name: analysis_details
    description: brief description of the analysis pipeline used for producing the
      asc_file; perhaps a link to something like a WDL file or github repository
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: analysis_details
    owner: Aligned_dna_short_read
    domain_of:
    - Aligned_dna_short_read
    - Called_variants_dna_short_read
    - Aligned_nanopore
    - Called_variants_nanopore
    - Aligned_pac_bio
    - Called_variants_pac_bio
    - Called_peaks_atac_short_read
    - Allele_specific_atac_short_read
    range: string
  quality_issues:
    name: quality_issues
    description: describe if there are any QC issues that would be important to note
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: quality_issues
    owner: Aligned_dna_short_read
    domain_of:
    - Analyte
    - Aligned_dna_short_read
    - Aligned_rna_short_read
    - Aligned_nanopore
    range: string