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Class: CalledVariantsPacBio

Table containing called_variants_pac_bio information

URI: gregor_linkml:CalledVariantsPacBio

classDiagram class CalledVariantsPacBio click CalledVariantsPacBio href "../CalledVariantsPacBio" CalledVariantsPacBio : aligned_pac_bio_set_id CalledVariantsPacBio : analysis_details CalledVariantsPacBio : called_variants_dna_file CalledVariantsPacBio : called_variants_pac_bio_id CalledVariantsPacBio : caller_software CalledVariantsPacBio : md5sum CalledVariantsPacBio : variant_types

Slots

Name Cardinality and Range Description Inheritance
called_variants_pac_bio_id 1
String		 unique key for table (anvil requirement) direct
aligned_pac_bio_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:CalledVariantsPacBio
native gregor_linkml:CalledVariantsPacBio

LinkML Source

Direct

name: Called_variants_pac_bio
description: Table containing called_variants_pac_bio information
from_schema: https://w3id.org/madanucd/gregor_linkml
slots:
- called_variants_pac_bio_id
- aligned_pac_bio_set_id
- called_variants_dna_file
- md5sum
- caller_software
- variant_types
- analysis_details

Induced

name: Called_variants_pac_bio
description: Table containing called_variants_pac_bio information
from_schema: https://w3id.org/madanucd/gregor_linkml
attributes:
  called_variants_pac_bio_id:
    name: called_variants_pac_bio_id
    description: unique key for table (anvil requirement)
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    identifier: true
    alias: called_variants_pac_bio_id
    owner: Called_variants_pac_bio
    domain_of:
    - Called_variants_pac_bio
    range: string
    required: true
  aligned_pac_bio_set_id:
    name: aligned_pac_bio_set_id
    description: identifier for experiment set
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: aligned_pac_bio_set_id
    owner: Called_variants_pac_bio
    domain_of:
    - Aligned_pac_bio_set
    - Called_variants_pac_bio
    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_pac_bio
    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_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
  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_pac_bio
    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_pac_bio
    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_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