Class: CalledPeaksAtacShortRead

Table containing called_peaks_atac_short_read information

URI: gregor_linkml:CalledPeaksAtacShortRead

classDiagram class CalledPeaksAtacShortRead click CalledPeaksAtacShortRead href "../CalledPeaksAtacShortRead" CalledPeaksAtacShortRead : aligned_atac_short_read_id CalledPeaksAtacShortRead : analysis_details CalledPeaksAtacShortRead : called_peaks_atac_short_read_id CalledPeaksAtacShortRead : called_peaks_file CalledPeaksAtacShortRead : peak_caller_software CalledPeaksAtacShortRead : peak_set_type CalledPeaksAtacShortRead --> "1" PeakSetTypeEnum : peak_set_type click PeakSetTypeEnum href "../PeakSetTypeEnum" CalledPeaksAtacShortRead : peaks_md5sum

Slots

Name	Cardinality and Range	Description	Inheritance
called_peaks_atac_short_read_id	1 String	identifier for called peaks	direct
aligned_atac_short_read_id	1 String	identifier for aligned ATAC-seq data	direct
called_peaks_file	1 String	name and path of the bed file with open chromatin peaks after QC filtering	direct
peaks_md5sum	1 String	md5 checksum for called_peaks_file	direct
peak_caller_software	1..* String	peak calling software used including version number	direct
peak_set_type	1 PeakSetTypeEnum	peak set type, according to ENCODE descriptors	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:CalledPeaksAtacShortRead
native	gregor_linkml:CalledPeaksAtacShortRead

LinkML Source

Direct

name: Called_peaks_atac_short_read
description: Table containing called_peaks_atac_short_read information
from_schema: https://w3id.org/madanucd/gregor_linkml
slots:
- called_peaks_atac_short_read_id
- aligned_atac_short_read_id
- called_peaks_file
- peaks_md5sum
- peak_caller_software
- peak_set_type
- analysis_details

Induced

name: Called_peaks_atac_short_read
description: Table containing called_peaks_atac_short_read information
from_schema: https://w3id.org/madanucd/gregor_linkml
attributes:
  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: Called_peaks_atac_short_read
    domain_of:
    - Called_peaks_atac_short_read
    - Allele_specific_atac_short_read
    range: string
    required: true
  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: Called_peaks_atac_short_read
    domain_of:
    - Aligned_atac_short_read
    - Called_peaks_atac_short_read
    range: string
    required: true
  called_peaks_file:
    name: called_peaks_file
    description: name and path of the bed file with open chromatin peaks after QC
      filtering
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: called_peaks_file
    owner: Called_peaks_atac_short_read
    domain_of:
    - Called_peaks_atac_short_read
    range: string
    required: true
  peaks_md5sum:
    name: peaks_md5sum
    description: md5 checksum for called_peaks_file
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: peaks_md5sum
    owner: Called_peaks_atac_short_read
    domain_of:
    - Called_peaks_atac_short_read
    range: string
    required: true
  peak_caller_software:
    name: peak_caller_software
    description: peak calling software used including version number
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    multivalued: true
    alias: peak_caller_software
    owner: Called_peaks_atac_short_read
    domain_of:
    - Called_peaks_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: Called_peaks_atac_short_read
    domain_of:
    - Called_peaks_atac_short_read
    - Allele_specific_atac_short_read
    range: Peak_set_typeEnum
    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: Called_peaks_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