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Class: AlignedPacBio

Table containing aligned_pac_bio information

URI: gregor_linkml:AlignedPacBio

classDiagram class AlignedPacBio click AlignedPacBio href "../AlignedPacBio" AlignedPacBio : aligned_pac_bio_file AlignedPacBio : aligned_pac_bio_id AlignedPacBio : aligned_pac_bio_index_file AlignedPacBio : aligned_read_length_mean AlignedPacBio : alignment_software AlignedPacBio : analysis_details AlignedPacBio : contamination AlignedPacBio : experiment_pac_bio_id AlignedPacBio : genome_coverage AlignedPacBio : mapped_reads_pct AlignedPacBio : md5sum AlignedPacBio : mean_coverage AlignedPacBio : methylation_called AlignedPacBio : num_aligned_bases AlignedPacBio : num_aligned_reads AlignedPacBio : num_bases AlignedPacBio : num_reads AlignedPacBio : read_error_rate AlignedPacBio : read_length_mean AlignedPacBio : reference_assembly AlignedPacBio --> "1" ReferenceAssemblyEnum : reference_assembly click ReferenceAssemblyEnum href "../ReferenceAssemblyEnum" AlignedPacBio : sex_concordance

Slots

Name Cardinality and Range Description Inheritance
aligned_pac_bio_id 1
String		 direct
experiment_pac_bio_id 1
String		 identifier for experiment direct
aligned_pac_bio_file 1
String		 name and path of file with aligned reads direct
aligned_pac_bio_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
alignment_software 1
String		 Software including version number direct
analysis_details 0..1
String		 brief description of the analysis pipeline used for producing the asc_file; p... direct
mean_coverage 0..1
Float		 Mean coverage of either the genome or the targeted regions direct
genome_coverage 0..1
Integer		 e direct
contamination 0..1
Float		 Contamination level estimate direct
sex_concordance 0..1
Boolean		 Comparison between reported sex vs genotype sex; Other if ploidy NOT XX or XY... direct
num_reads 0..1
Integer		 Total reads (before/ignoring alignment) direct
num_bases 0..1
Integer		 Number of bases (before/ignoring alignment) direct
read_length_mean 0..1
Integer		 Mean length of all reads (before/ignoring alignment) direct
num_aligned_reads 0..1
Integer		 Total aligned reads direct
num_aligned_bases 0..1
Integer		 Number of bases in aligned reads direct
aligned_read_length_mean 0..1
Integer		 Mean length of aligned reads direct
read_error_rate 0..1
Float		 Mean empirical per-base error rate of aligned reads direct
mapped_reads_pct 0..1
Float		 Number between 1 and 100, na direct
methylation_called 1
Boolean		 Indicates whether 5mC methylation has been called and annotated in the BAM fi... direct

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Aligned_pac_bio
description: Table containing aligned_pac_bio information
from_schema: https://w3id.org/madanucd/gregor_linkml
slots:
- aligned_pac_bio_id
- experiment_pac_bio_id
- aligned_pac_bio_file
- aligned_pac_bio_index_file
- md5sum
- reference_assembly
- alignment_software
- analysis_details
- mean_coverage
- genome_coverage
- contamination
- sex_concordance
- num_reads
- num_bases
- read_length_mean
- num_aligned_reads
- num_aligned_bases
- aligned_read_length_mean
- read_error_rate
- mapped_reads_pct
- methylation_called

Induced

name: Aligned_pac_bio
description: Table containing aligned_pac_bio information
from_schema: https://w3id.org/madanucd/gregor_linkml
attributes:
  aligned_pac_bio_id:
    name: aligned_pac_bio_id
    description: ''
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: aligned_pac_bio_id
    owner: Aligned_pac_bio
    domain_of:
    - Aligned_pac_bio
    - Aligned_pac_bio_set
    range: string
    required: true
  experiment_pac_bio_id:
    name: experiment_pac_bio_id
    description: identifier for experiment
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: experiment_pac_bio_id
    owner: Aligned_pac_bio
    domain_of:
    - Experiment_pac_bio
    - Aligned_pac_bio
    range: string
    required: true
  aligned_pac_bio_file:
    name: aligned_pac_bio_file
    description: name and path of file with aligned reads
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: aligned_pac_bio_file
    owner: Aligned_pac_bio
    domain_of:
    - Aligned_pac_bio
    range: string
    required: true
  aligned_pac_bio_index_file:
    name: aligned_pac_bio_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_pac_bio_index_file
    owner: Aligned_pac_bio
    domain_of:
    - Aligned_pac_bio
    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_pac_bio
    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_pac_bio
    domain_of:
    - Aligned_dna_short_read
    - Aligned_rna_short_read
    - Aligned_nanopore
    - Aligned_pac_bio
    - Aligned_atac_short_read
    range: Reference_assemblyEnum
    required: true
  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_pac_bio
    domain_of:
    - Aligned_dna_short_read
    - Aligned_rna_short_read
    - Aligned_nanopore
    - Aligned_pac_bio
    - Aligned_atac_short_read
    range: string
    required: true
  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_pac_bio
    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
  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_pac_bio
    domain_of:
    - Aligned_dna_short_read
    - Aligned_rna_short_read
    - Aligned_nanopore
    - Aligned_pac_bio
    - Aligned_atac_short_read
    range: float
  genome_coverage:
    name: genome_coverage
    description: e.g. ≥90% at 10x or 20x; per consortium decision
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: genome_coverage
    owner: Aligned_pac_bio
    domain_of:
    - Aligned_nanopore
    - Aligned_pac_bio
    range: integer
  contamination:
    name: contamination
    description: Contamination level estimate., e.g. <1% (display raw fraction not
      percent)
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: contamination
    owner: Aligned_pac_bio
    domain_of:
    - Aligned_nanopore
    - Aligned_pac_bio
    range: float
  sex_concordance:
    name: sex_concordance
    description: Comparison between reported sex vs genotype sex; Other if ploidy
      NOT XX or XY and Other if sex at birth is not known, thus unable to perform
      sex concordance
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: sex_concordance
    owner: Aligned_pac_bio
    domain_of:
    - Aligned_nanopore
    - Aligned_pac_bio
    range: boolean
  num_reads:
    name: num_reads
    description: Total reads (before/ignoring alignment)
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: num_reads
    owner: Aligned_pac_bio
    domain_of:
    - Aligned_nanopore
    - Aligned_pac_bio
    range: integer
  num_bases:
    name: num_bases
    description: Number of bases (before/ignoring alignment)
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: num_bases
    owner: Aligned_pac_bio
    domain_of:
    - Aligned_nanopore
    - Aligned_pac_bio
    range: integer
  read_length_mean:
    name: read_length_mean
    description: Mean length of all reads (before/ignoring alignment)
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: read_length_mean
    owner: Aligned_pac_bio
    domain_of:
    - Aligned_nanopore
    - Aligned_pac_bio
    range: integer
  num_aligned_reads:
    name: num_aligned_reads
    description: Total aligned reads
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: num_aligned_reads
    owner: Aligned_pac_bio
    domain_of:
    - Aligned_nanopore
    - Aligned_pac_bio
    range: integer
  num_aligned_bases:
    name: num_aligned_bases
    description: Number of bases in aligned reads
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: num_aligned_bases
    owner: Aligned_pac_bio
    domain_of:
    - Aligned_nanopore
    - Aligned_pac_bio
    range: integer
  aligned_read_length_mean:
    name: aligned_read_length_mean
    description: Mean length of aligned reads
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: aligned_read_length_mean
    owner: Aligned_pac_bio
    domain_of:
    - Aligned_nanopore
    - Aligned_pac_bio
    range: integer
  read_error_rate:
    name: read_error_rate
    description: Mean empirical per-base error rate of aligned reads
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: read_error_rate
    owner: Aligned_pac_bio
    domain_of:
    - Aligned_nanopore
    - Aligned_pac_bio
    range: float
  mapped_reads_pct:
    name: mapped_reads_pct
    description: Number between 1 and 100, na
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: mapped_reads_pct
    owner: Aligned_pac_bio
    domain_of:
    - Aligned_nanopore
    - Aligned_pac_bio
    range: float
  methylation_called:
    name: methylation_called
    description: Indicates whether 5mC methylation has been called and annotated in
      the BAM file's MM and ML tags
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: methylation_called
    owner: Aligned_pac_bio
    domain_of:
    - Aligned_nanopore
    - Aligned_pac_bio
    range: boolean
    required: true