Class: AlignedRnaShortRead

Table containing aligned_rna_short_read information

classDiagram class AlignedRnaShortRead click AlignedRnaShortRead href "../AlignedRnaShortRead" AlignedRnaShortRead : aligned_rna_short_read_file AlignedRnaShortRead : aligned_rna_short_read_id AlignedRnaShortRead : aligned_rna_short_read_index_file AlignedRnaShortRead : alignment_log_file AlignedRnaShortRead : alignment_postprocessing AlignedRnaShortRead : alignment_software AlignedRnaShortRead : experiment_rna_short_read_id AlignedRnaShortRead : gene_annotation AlignedRnaShortRead : gene_annotation_details AlignedRnaShortRead --> "0..1" GeneAnnotationDetailsEnum : gene_annotation_details click GeneAnnotationDetailsEnum href "../GeneAnnotationDetailsEnum" AlignedRnaShortRead : md5sum AlignedRnaShortRead : mean_coverage AlignedRnaShortRead : percent_multimapped AlignedRnaShortRead : percent_unaligned AlignedRnaShortRead : percent_uniquely_aligned AlignedRnaShortRead : quality_issues AlignedRnaShortRead : reference_assembly AlignedRnaShortRead --> "1" ReferenceAssemblyEnum : reference_assembly click ReferenceAssemblyEnum href "../ReferenceAssemblyEnum" AlignedRnaShortRead : reference_assembly_details AlignedRnaShortRead : reference_assembly_uri

Slots

Name	Cardinality and Range	Description	Inheritance
aligned_rna_short_read_id	1 String	identifier for aligned_short_read (primary key)	direct
experiment_rna_short_read_id	1 String	identifier for experiment	direct
aligned_rna_short_read_file	1 String	name and path of file with aligned reads	direct
aligned_rna_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
gene_annotation	1 String	annotation file used for alignment	direct
gene_annotation_details	0..1 GeneAnnotationDetailsEnum		direct
alignment_software	1 String	Software including version number	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
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:AlignedRnaShortRead
native	gregor_linkml:AlignedRnaShortRead

LinkML Source

Direct

name: Aligned_rna_short_read
description: Table containing aligned_rna_short_read information
from_schema: https://w3id.org/madanucd/gregor_linkml
slots:
- aligned_rna_short_read_id
- experiment_rna_short_read_id
- aligned_rna_short_read_file
- aligned_rna_short_read_index_file
- md5sum
- reference_assembly
- reference_assembly_uri
- reference_assembly_details
- gene_annotation
- gene_annotation_details
- alignment_software
- alignment_log_file
- alignment_postprocessing
- mean_coverage
- percent_uniquely_aligned
- percent_multimapped
- percent_unaligned
- quality_issues

Induced

name: Aligned_rna_short_read
description: Table containing aligned_rna_short_read information
from_schema: https://w3id.org/madanucd/gregor_linkml
attributes:
  aligned_rna_short_read_id:
    name: aligned_rna_short_read_id
    description: identifier for aligned_short_read (primary key)
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    identifier: true
    alias: aligned_rna_short_read_id
    owner: Aligned_rna_short_read
    domain_of:
    - Aligned_rna_short_read
    range: string
    required: true
  experiment_rna_short_read_id:
    name: experiment_rna_short_read_id
    description: identifier for experiment
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: experiment_rna_short_read_id
    owner: Aligned_rna_short_read
    domain_of:
    - Experiment_rna_short_read
    - Aligned_rna_short_read
    range: string
    required: true
  aligned_rna_short_read_file:
    name: aligned_rna_short_read_file
    description: name and path of file with aligned reads
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: aligned_rna_short_read_file
    owner: Aligned_rna_short_read
    domain_of:
    - Aligned_rna_short_read
    range: string
    required: true
  aligned_rna_short_read_index_file:
    name: aligned_rna_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_rna_short_read_index_file
    owner: Aligned_rna_short_read
    domain_of:
    - Aligned_rna_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_rna_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_rna_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_rna_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_rna_short_read
    domain_of:
    - Aligned_dna_short_read
    - Aligned_rna_short_read
    - Aligned_atac_short_read
    range: string
  gene_annotation:
    name: gene_annotation
    description: annotation file used for alignment
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: gene_annotation
    owner: Aligned_rna_short_read
    domain_of:
    - Aligned_rna_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_rna_short_read
    domain_of:
    - Aligned_rna_short_read
    - Aligned_atac_short_read
    range: Gene_annotation_detailsEnum
  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_rna_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
  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_rna_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_rna_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_rna_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_rna_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_rna_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_rna_short_read
    domain_of:
    - Aligned_rna_short_read
    - Aligned_atac_short_read
    range: float
  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_rna_short_read
    domain_of:
    - Analyte
    - Aligned_dna_short_read
    - Aligned_rna_short_read
    - Aligned_nanopore
    range: string