Class: AlleleSpecificAtacShortRead

Table containing allele_specific_atac_short_read information

URI: gregor_linkml:AlleleSpecificAtacShortRead

classDiagram class AlleleSpecificAtacShortRead click AlleleSpecificAtacShortRead href "../AlleleSpecificAtacShortRead" AlleleSpecificAtacShortRead : analysis_details AlleleSpecificAtacShortRead : asc_atac_short_read_id AlleleSpecificAtacShortRead : asc_file AlleleSpecificAtacShortRead : asc_md5sum AlleleSpecificAtacShortRead : called_peaks_atac_short_read_id AlleleSpecificAtacShortRead : het_sites_file AlleleSpecificAtacShortRead : het_sites_md5sum AlleleSpecificAtacShortRead : peak_set_type AlleleSpecificAtacShortRead --> "1" PeakSetTypeEnum : peak_set_type click PeakSetTypeEnum href "../PeakSetTypeEnum"

Slots

Name	Cardinality and Range	Description	Inheritance
asc_atac_short_read_id	0..1 String	unique key for table (anvil requirement)	direct
called_peaks_atac_short_read_id	1 String	identifier for called peaks	direct
asc_file	1 String	name and path of the tsv file with allele-specific chromatin accessibility me...	direct
asc_md5sum	1 String	md5 checksum for called_peaks_file	direct
peak_set_type	1 PeakSetTypeEnum	peak set type, according to ENCODE descriptors	direct
het_sites_file	1 String	VCF file containing prefiltered heterozygous sites used for reference alignme...	direct
het_sites_md5sum	1 String	md5 checksum for het_sites_file	direct
analysis_details	0..1 String	brief description of the analysis pipeline used for producing the asc_file; p...	direct

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Allele_specific_atac_short_read
description: Table containing allele_specific_atac_short_read information
from_schema: https://w3id.org/madanucd/gregor_linkml
slots:
- asc_atac_short_read_id
- called_peaks_atac_short_read_id
- asc_file
- asc_md5sum
- peak_set_type
- het_sites_file
- het_sites_md5sum
- analysis_details

Induced

name: Allele_specific_atac_short_read
description: Table containing allele_specific_atac_short_read information
from_schema: https://w3id.org/madanucd/gregor_linkml
attributes:
  asc_atac_short_read_id:
    name: asc_atac_short_read_id
    description: unique key for table (anvil requirement)
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: asc_atac_short_read_id
    owner: Allele_specific_atac_short_read
    domain_of:
    - Allele_specific_atac_short_read
    range: string
  called_peaks_atac_short_read_id:
    name: called_peaks_atac_short_read_id
    description: identifier for called peaks
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: called_peaks_atac_short_read_id
    owner: Allele_specific_atac_short_read
    domain_of:
    - Called_peaks_atac_short_read
    - Allele_specific_atac_short_read
    range: string
    required: true
  asc_file:
    name: asc_file
    description: name and path of the tsv file with allele-specific chromatin accessibility
      measures (logFC) at heterozygous sites after QC and significance testing
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: asc_file
    owner: Allele_specific_atac_short_read
    domain_of:
    - Allele_specific_atac_short_read
    range: string
    required: true
  asc_md5sum:
    name: asc_md5sum
    description: md5 checksum for called_peaks_file
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: asc_md5sum
    owner: Allele_specific_atac_short_read
    domain_of:
    - Allele_specific_atac_short_read
    range: string
    required: true
  peak_set_type:
    name: peak_set_type
    description: peak set type, according to ENCODE descriptors
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: peak_set_type
    owner: Allele_specific_atac_short_read
    domain_of:
    - Called_peaks_atac_short_read
    - Allele_specific_atac_short_read
    range: Peak_set_typeEnum
    required: true
  het_sites_file:
    name: het_sites_file
    description: VCF file containing prefiltered heterozygous sites used for reference
      alignment bias testing and calling allele-specific chromatin accessibility events
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: het_sites_file
    owner: Allele_specific_atac_short_read
    domain_of:
    - Allele_specific_atac_short_read
    range: string
    required: true
  het_sites_md5sum:
    name: het_sites_md5sum
    description: md5 checksum for het_sites_file
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: het_sites_md5sum
    owner: Allele_specific_atac_short_read
    domain_of:
    - Allele_specific_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: Allele_specific_atac_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