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Class: AlignedAtacShortRead

Table containing aligned_atac_short_read information

URI: gregor_linkml:AlignedAtacShortRead

classDiagram class AlignedAtacShortRead click AlignedAtacShortRead href "../AlignedAtacShortRead" AlignedAtacShortRead : aligned_atac_short_read_file AlignedAtacShortRead : aligned_atac_short_read_id AlignedAtacShortRead : aligned_atac_short_read_index_file AlignedAtacShortRead : alignment_log_file AlignedAtacShortRead : alignment_postprocessing AlignedAtacShortRead : alignment_software AlignedAtacShortRead : experiment_atac_short_read_id AlignedAtacShortRead : gene_annotation_details AlignedAtacShortRead --> "0..1" GeneAnnotationDetailsEnum : gene_annotation_details click GeneAnnotationDetailsEnum href "../GeneAnnotationDetailsEnum" AlignedAtacShortRead : md5sum AlignedAtacShortRead : mean_coverage AlignedAtacShortRead : percent_multimapped AlignedAtacShortRead : percent_unaligned AlignedAtacShortRead : percent_uniquely_aligned AlignedAtacShortRead : reference_assembly AlignedAtacShortRead --> "1" ReferenceAssemblyEnum : reference_assembly click ReferenceAssemblyEnum href "../ReferenceAssemblyEnum" AlignedAtacShortRead : reference_assembly_details AlignedAtacShortRead : reference_assembly_uri

Slots

Name Cardinality and Range Description Inheritance
aligned_atac_short_read_id 1
String		 identifier for aligned ATAC-seq data direct
experiment_atac_short_read_id 1
String		 identifier for experiment direct
aligned_atac_short_read_file 1
String		 name and path of file with aligned reads direct
aligned_atac_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
gene_annotation_details 0..1
GeneAnnotationDetailsEnum		 direct
alignment_log_file 0..1
String		 path of (log) file with all parameters for alignment software direct
alignment_postprocessing 0..1
String		 If any post processing was applied direct
mean_coverage 0..1
Float		 Mean coverage of either the genome or the targeted regions direct
percent_uniquely_aligned 0..1
Float		 how many reads aligned to just one place direct
percent_multimapped 0..1
Float		 how many reads aligned to multiple places direct
percent_unaligned 0..1
Float		 how many reads didn't align direct

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Aligned_atac_short_read
description: Table containing aligned_atac_short_read information
from_schema: https://w3id.org/madanucd/gregor_linkml
slots:
- aligned_atac_short_read_id
- experiment_atac_short_read_id
- aligned_atac_short_read_file
- aligned_atac_short_read_index_file
- md5sum
- reference_assembly
- reference_assembly_uri
- reference_assembly_details
- alignment_software
- gene_annotation_details
- alignment_log_file
- alignment_postprocessing
- mean_coverage
- percent_uniquely_aligned
- percent_multimapped
- percent_unaligned

Induced

name: Aligned_atac_short_read
description: Table containing aligned_atac_short_read information
from_schema: https://w3id.org/madanucd/gregor_linkml
attributes:
  aligned_atac_short_read_id:
    name: aligned_atac_short_read_id
    description: identifier for aligned ATAC-seq data
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: aligned_atac_short_read_id
    owner: Aligned_atac_short_read
    domain_of:
    - Aligned_atac_short_read
    - Called_peaks_atac_short_read
    range: string
    required: true
  experiment_atac_short_read_id:
    name: experiment_atac_short_read_id
    description: identifier for experiment
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: experiment_atac_short_read_id
    owner: Aligned_atac_short_read
    domain_of:
    - Experiment_atac_short_read
    - Aligned_atac_short_read
    range: string
    required: true
  aligned_atac_short_read_file:
    name: aligned_atac_short_read_file
    description: name and path of file with aligned reads
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: aligned_atac_short_read_file
    owner: Aligned_atac_short_read
    domain_of:
    - Aligned_atac_short_read
    range: string
    required: true
  aligned_atac_short_read_index_file:
    name: aligned_atac_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_atac_short_read_index_file
    owner: Aligned_atac_short_read
    domain_of:
    - Aligned_atac_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_atac_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_atac_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_atac_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_atac_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_atac_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
  gene_annotation_details:
    name: gene_annotation_details
    description: ''
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: gene_annotation_details
    owner: Aligned_atac_short_read
    domain_of:
    - Aligned_rna_short_read
    - Aligned_atac_short_read
    range: Gene_annotation_detailsEnum
  alignment_log_file:
    name: alignment_log_file
    description: path of (log) file with all parameters for alignment software
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: alignment_log_file
    owner: Aligned_atac_short_read
    domain_of:
    - Aligned_rna_short_read
    - Aligned_atac_short_read
    range: string
  alignment_postprocessing:
    name: alignment_postprocessing
    description: If any post processing was applied
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: alignment_postprocessing
    owner: Aligned_atac_short_read
    domain_of:
    - Aligned_rna_short_read
    - Aligned_atac_short_read
    range: string
  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_atac_short_read
    domain_of:
    - Aligned_dna_short_read
    - Aligned_rna_short_read
    - Aligned_nanopore
    - Aligned_pac_bio
    - Aligned_atac_short_read
    range: float
  percent_uniquely_aligned:
    name: percent_uniquely_aligned
    description: how many reads aligned to just one place
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: percent_uniquely_aligned
    owner: Aligned_atac_short_read
    domain_of:
    - Aligned_rna_short_read
    - Aligned_atac_short_read
    range: float
  percent_multimapped:
    name: percent_multimapped
    description: how many reads aligned to multiple places
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: percent_multimapped
    owner: Aligned_atac_short_read
    domain_of:
    - Aligned_rna_short_read
    - Aligned_atac_short_read
    range: float
  percent_unaligned:
    name: percent_unaligned
    description: how many reads didn't align
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: percent_unaligned
    owner: Aligned_atac_short_read
    domain_of:
    - Aligned_rna_short_read
    - Aligned_atac_short_read
    range: float