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Class: ExperimentPacBio

Table containing experiment_pac_bio information

URI: gregor_linkml:ExperimentPacBio

classDiagram class ExperimentPacBio click ExperimentPacBio href "../ExperimentPacBio" ExperimentPacBio : analyte_id ExperimentPacBio : application_kit ExperimentPacBio --> "0..1" ApplicationKitEnum : application_kit click ApplicationKitEnum href "../ApplicationKitEnum" ExperimentPacBio : barcode_kit ExperimentPacBio : by_strand ExperimentPacBio : date_data_generation ExperimentPacBio : experiment_pac_bio_id ExperimentPacBio : experiment_sample_id ExperimentPacBio : experiment_type ExperimentPacBio --> "1" ExperimentTypeEnum : experiment_type click ExperimentTypeEnum href "../ExperimentTypeEnum" ExperimentPacBio : fragmentation_method ExperimentPacBio : includes_CpG_methylation ExperimentPacBio : includes_kinetics ExperimentPacBio : instrument_ics_version ExperimentPacBio : library_size ExperimentPacBio : movie_length_hours ExperimentPacBio : movie_name ExperimentPacBio : polymerase_kit ExperimentPacBio : seq_library_prep_kit_method ExperimentPacBio : sequencing_kit ExperimentPacBio : sequencing_platform ExperimentPacBio : size_selection_method ExperimentPacBio : smrt_cell_id ExperimentPacBio : smrt_cell_kit ExperimentPacBio : smrtlink_server_version ExperimentPacBio : targeted_region_bed_file ExperimentPacBio : targeted_regions_method ExperimentPacBio : was_barcoded

Slots

Name Cardinality and Range Description Inheritance
experiment_pac_bio_id 1
String		 identifier for experiment direct
analyte_id 1
String		 direct
experiment_sample_id 0..1
String		 identifier used in the data file (e direct
seq_library_prep_kit_method 0..1
String		 Library prep kit used direct
fragmentation_method 0..1
String		 method used for shearing/fragmentation direct
experiment_type 1
ExperimentTypeEnum		 direct
targeted_regions_method 0..1
String		 Which capture kit is used direct
targeted_region_bed_file 0..1
String		 name and path of bed file uploaded to workspace direct
date_data_generation 0..1
Date		 Date of data generation (First sequencing date) direct
sequencing_platform 0..1
String		 sequencing platform used for the experiment direct
was_barcoded 1
Boolean		 indicates whether samples were barcoded on this flowcell direct
barcode_kit 0..1
String		 Barcode kit used direct
application_kit 0..1
ApplicationKitEnum		 Library prep kits for special applications direct
smrtlink_server_version 1
String		 Version number of PacBio SMRTLink software direct
instrument_ics_version 1
String		 Version number of PacBio instrument control software direct
size_selection_method 0..1
String		 library prep - method use for library size selection direct
library_size 0..1
String		 library prep - expected size of library from FemtoPulse direct
smrt_cell_kit 0..1
String		 sequencing - part number of the SMRT Cell direct
smrt_cell_id 0..1
String		 sequencing - unique serial number for SMRT Cell direct
movie_name 0..1
String		 sequencing - unique name of sequencing collection direct
polymerase_kit 0..1
String		 sequencing - part number of polymerase kit used direct
sequencing_kit 0..1
String		 sequencing - part number of sequencing kit reagents direct
movie_length_hours 0..1
Float		 sequencing - length of sequencing collection, in hrs direct
includes_kinetics 0..1
Boolean		 run reports base kinetics direct
includes_CpG_methylation 0..1
Boolean		 run reports CpG methylation direct
by_strand 0..1
Boolean		 run reports separate reads per strand direct

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Experiment_pac_bio
description: Table containing experiment_pac_bio information
from_schema: https://w3id.org/madanucd/gregor_linkml
slots:
- experiment_pac_bio_id
- analyte_id
- experiment_sample_id
- seq_library_prep_kit_method
- fragmentation_method
- experiment_type
- targeted_regions_method
- targeted_region_bed_file
- date_data_generation
- sequencing_platform
- was_barcoded
- barcode_kit
- application_kit
- smrtlink_server_version
- instrument_ics_version
- size_selection_method
- library_size
- smrt_cell_kit
- smrt_cell_id
- movie_name
- polymerase_kit
- sequencing_kit
- movie_length_hours
- includes_kinetics
- includes_CpG_methylation
- by_strand

Induced

name: Experiment_pac_bio
description: Table containing experiment_pac_bio information
from_schema: https://w3id.org/madanucd/gregor_linkml
attributes:
  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: Experiment_pac_bio
    domain_of:
    - Experiment_pac_bio
    - Aligned_pac_bio
    range: string
    required: true
  analyte_id:
    name: analyte_id
    description: ''
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: analyte_id
    owner: Experiment_pac_bio
    domain_of:
    - Analyte
    - Experiment_dna_short_read
    - Experiment_rna_short_read
    - Experiment_nanopore
    - Experiment_pac_bio
    - Experiment_atac_short_read
    range: string
    required: true
  experiment_sample_id:
    name: experiment_sample_id
    description: identifier used in the data file (e.g. the SM tag in a BAM header,
      column headers for genotype fields in a VCF file)
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: experiment_sample_id
    owner: Experiment_pac_bio
    domain_of:
    - Experiment_dna_short_read
    - Experiment_rna_short_read
    - Experiment_nanopore
    - Experiment_pac_bio
    - Experiment_atac_short_read
    range: string
  seq_library_prep_kit_method:
    name: seq_library_prep_kit_method
    description: Library prep kit used
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: seq_library_prep_kit_method
    owner: Experiment_pac_bio
    domain_of:
    - Experiment_dna_short_read
    - Experiment_rna_short_read
    - Experiment_nanopore
    - Experiment_pac_bio
    - Experiment_atac_short_read
    range: string
  fragmentation_method:
    name: fragmentation_method
    description: method used for shearing/fragmentation
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: fragmentation_method
    owner: Experiment_pac_bio
    domain_of:
    - Experiment_nanopore
    - Experiment_pac_bio
    range: string
  experiment_type:
    name: experiment_type
    description: ''
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: experiment_type
    owner: Experiment_pac_bio
    domain_of:
    - Experiment_dna_short_read
    - Experiment_rna_short_read
    - Experiment_nanopore
    - Experiment_pac_bio
    - Experiment_atac_short_read
    range: Experiment_typeEnum
    required: true
  targeted_regions_method:
    name: targeted_regions_method
    description: Which capture kit is used. Can be missing if RC receives external
      data
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: targeted_regions_method
    owner: Experiment_pac_bio
    domain_of:
    - Experiment_dna_short_read
    - Experiment_nanopore
    - Experiment_pac_bio
    - Experiment_atac_short_read
    range: string
  targeted_region_bed_file:
    name: targeted_region_bed_file
    description: name and path of bed file uploaded to workspace
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: targeted_region_bed_file
    owner: Experiment_pac_bio
    domain_of:
    - Experiment_dna_short_read
    - Experiment_nanopore
    - Experiment_pac_bio
    - Experiment_atac_short_read
    range: string
  date_data_generation:
    name: date_data_generation
    description: Date of data generation (First sequencing date)
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: date_data_generation
    owner: Experiment_pac_bio
    domain_of:
    - Experiment_dna_short_read
    - Experiment_rna_short_read
    - Experiment_nanopore
    - Experiment_pac_bio
    - Experiment_atac_short_read
    range: date
  sequencing_platform:
    name: sequencing_platform
    description: sequencing platform used for the experiment
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: sequencing_platform
    owner: Experiment_pac_bio
    domain_of:
    - Experiment_dna_short_read
    - Experiment_rna_short_read
    - Experiment_nanopore
    - Experiment_pac_bio
    - Experiment_atac_short_read
    range: string
  was_barcoded:
    name: was_barcoded
    description: indicates whether samples were barcoded on this flowcell
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: was_barcoded
    owner: Experiment_pac_bio
    domain_of:
    - Experiment_nanopore
    - Experiment_pac_bio
    range: boolean
    required: true
  barcode_kit:
    name: barcode_kit
    description: Barcode kit used
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: barcode_kit
    owner: Experiment_pac_bio
    domain_of:
    - Experiment_nanopore
    - Experiment_pac_bio
    range: string
  application_kit:
    name: application_kit
    description: Library prep kits for special applications
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: application_kit
    owner: Experiment_pac_bio
    domain_of:
    - Experiment_pac_bio
    range: Application_kitEnum
  smrtlink_server_version:
    name: smrtlink_server_version
    description: Version number of PacBio SMRTLink software
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: smrtlink_server_version
    owner: Experiment_pac_bio
    domain_of:
    - Experiment_pac_bio
    range: string
    required: true
  instrument_ics_version:
    name: instrument_ics_version
    description: Version number of PacBio instrument control software
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: instrument_ics_version
    owner: Experiment_pac_bio
    domain_of:
    - Experiment_pac_bio
    range: string
    required: true
  size_selection_method:
    name: size_selection_method
    description: library prep - method use for library size selection
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: size_selection_method
    owner: Experiment_pac_bio
    domain_of:
    - Experiment_pac_bio
    range: string
  library_size:
    name: library_size
    description: library prep - expected size of library from FemtoPulse
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: library_size
    owner: Experiment_pac_bio
    domain_of:
    - Experiment_pac_bio
    range: string
  smrt_cell_kit:
    name: smrt_cell_kit
    description: sequencing - part number of the SMRT Cell
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: smrt_cell_kit
    owner: Experiment_pac_bio
    domain_of:
    - Experiment_pac_bio
    range: string
  smrt_cell_id:
    name: smrt_cell_id
    description: sequencing - unique serial number for SMRT Cell
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: smrt_cell_id
    owner: Experiment_pac_bio
    domain_of:
    - Experiment_pac_bio
    range: string
  movie_name:
    name: movie_name
    description: sequencing - unique name of sequencing collection
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: movie_name
    owner: Experiment_pac_bio
    domain_of:
    - Experiment_pac_bio
    range: string
  polymerase_kit:
    name: polymerase_kit
    description: sequencing - part number of polymerase kit used
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: polymerase_kit
    owner: Experiment_pac_bio
    domain_of:
    - Experiment_pac_bio
    range: string
  sequencing_kit:
    name: sequencing_kit
    description: sequencing - part number of sequencing kit reagents
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: sequencing_kit
    owner: Experiment_pac_bio
    domain_of:
    - Experiment_pac_bio
    range: string
  movie_length_hours:
    name: movie_length_hours
    description: sequencing - length of sequencing collection, in hrs
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: movie_length_hours
    owner: Experiment_pac_bio
    domain_of:
    - Experiment_pac_bio
    range: float
  includes_kinetics:
    name: includes_kinetics
    description: run reports base kinetics
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: includes_kinetics
    owner: Experiment_pac_bio
    domain_of:
    - Experiment_pac_bio
    range: boolean
  includes_CpG_methylation:
    name: includes_CpG_methylation
    description: run reports CpG methylation
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: includes_CpG_methylation
    owner: Experiment_pac_bio
    domain_of:
    - Experiment_pac_bio
    range: boolean
  by_strand:
    name: by_strand
    description: run reports separate reads per strand
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: by_strand
    owner: Experiment_pac_bio
    domain_of:
    - Experiment_pac_bio
    range: boolean