Class: CalledVariantsDnaShortRead

Table containing called_variants_dna_short_read information

URI: gregor_linkml:CalledVariantsDnaShortRead

classDiagram class CalledVariantsDnaShortRead click CalledVariantsDnaShortRead href "../CalledVariantsDnaShortRead" CalledVariantsDnaShortRead : aligned_dna_short_read_set_id CalledVariantsDnaShortRead : analysis_details CalledVariantsDnaShortRead : called_variants_dna_file CalledVariantsDnaShortRead : called_variants_dna_short_read_id CalledVariantsDnaShortRead : caller_software CalledVariantsDnaShortRead : md5sum CalledVariantsDnaShortRead : variant_types

Slots

Name	Cardinality and Range	Description	Inheritance
called_variants_dna_short_read_id	1 String	unique key for table (anvil requirement)	direct
aligned_dna_short_read_set_id	1 String	identifier for experiment set	direct
called_variants_dna_file	1 String	name and path of the file with variant calls	direct
md5sum	1 String	md5 checksum for file	direct
caller_software	1..* String	variant calling software used including version number	direct
variant_types	1..* String	types of variants called	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:CalledVariantsDnaShortRead
native	gregor_linkml:CalledVariantsDnaShortRead

LinkML Source

Direct

name: Called_variants_dna_short_read
description: Table containing called_variants_dna_short_read information
from_schema: https://w3id.org/madanucd/gregor_linkml
slots:
- called_variants_dna_short_read_id
- aligned_dna_short_read_set_id
- called_variants_dna_file
- md5sum
- caller_software
- variant_types
- analysis_details

Induced

name: Called_variants_dna_short_read
description: Table containing called_variants_dna_short_read information
from_schema: https://w3id.org/madanucd/gregor_linkml
attributes:
  called_variants_dna_short_read_id:
    name: called_variants_dna_short_read_id
    description: unique key for table (anvil requirement)
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    identifier: true
    alias: called_variants_dna_short_read_id
    owner: Called_variants_dna_short_read
    domain_of:
    - Called_variants_dna_short_read
    range: string
    required: true
  aligned_dna_short_read_set_id:
    name: aligned_dna_short_read_set_id
    description: identifier for experiment set
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: aligned_dna_short_read_set_id
    owner: Called_variants_dna_short_read
    domain_of:
    - Aligned_dna_short_read_set
    - Called_variants_dna_short_read
    range: string
    required: true
  called_variants_dna_file:
    name: called_variants_dna_file
    description: name and path of the file with variant calls
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: called_variants_dna_file
    owner: Called_variants_dna_short_read
    domain_of:
    - Called_variants_dna_short_read
    - Called_variants_nanopore
    - Called_variants_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: Called_variants_dna_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
  caller_software:
    name: caller_software
    description: variant calling software used including version number
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    multivalued: true
    alias: caller_software
    owner: Called_variants_dna_short_read
    domain_of:
    - Called_variants_dna_short_read
    - Called_variants_nanopore
    - Called_variants_pac_bio
    range: string
    required: true
  variant_types:
    name: variant_types
    description: types of variants called
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    multivalued: true
    alias: variant_types
    owner: Called_variants_dna_short_read
    domain_of:
    - Called_variants_dna_short_read
    - Called_variants_nanopore
    - Called_variants_pac_bio
    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: Called_variants_dna_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