Class: ExperimentRnaShortRead

Table containing experiment_rna_short_read information

URI: gregor_linkml:ExperimentRnaShortRead

classDiagram class ExperimentRnaShortRead click ExperimentRnaShortRead href "../ExperimentRnaShortRead" ExperimentRnaShortRead : 5prime3prime_bias ExperimentRnaShortRead : analyte_id ExperimentRnaShortRead : date_data_generation ExperimentRnaShortRead : estimated_library_size ExperimentRnaShortRead : experiment_rna_short_read_id ExperimentRnaShortRead : experiment_sample_id ExperimentRnaShortRead : experiment_type ExperimentRnaShortRead --> "1" ExperimentTypeEnum : experiment_type click ExperimentTypeEnum href "../ExperimentTypeEnum" ExperimentRnaShortRead : library_prep_type ExperimentRnaShortRead --> "*" LibraryPrepTypeEnum : library_prep_type click LibraryPrepTypeEnum href "../LibraryPrepTypeEnum" ExperimentRnaShortRead : percent_chrX_Y ExperimentRnaShortRead : percent_GC ExperimentRnaShortRead : percent_Globin ExperimentRnaShortRead : percent_mRNA ExperimentRnaShortRead : percent_mtRNA ExperimentRnaShortRead : percent_rRNA ExperimentRnaShortRead : percent_UMI ExperimentRnaShortRead : read_length ExperimentRnaShortRead : RIN ExperimentRnaShortRead : seq_library_prep_kit_method ExperimentRnaShortRead : sequencing_platform ExperimentRnaShortRead : single_or_paired_ends ExperimentRnaShortRead --> "1" SingleOrPairedEndsEnum : single_or_paired_ends click SingleOrPairedEndsEnum href "../SingleOrPairedEndsEnum" ExperimentRnaShortRead : total_reads ExperimentRnaShortRead : within_site_batch_name

Slots

Name	Cardinality and Range	Description	Inheritance
experiment_rna_short_read_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
library_prep_type	* LibraryPrepTypeEnum	type of library prep	direct
experiment_type	1 ExperimentTypeEnum		direct
read_length	0..1 Integer	sequenced read length (bp); GREGoR RCs do paired end sequencing, so is the ex...	direct
single_or_paired_ends	1 SingleOrPairedEndsEnum	single or paired end	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
within_site_batch_name	1 String	batch number for the site, important for future batch correction	direct
RIN	0..1 Float	RIN number for quality of sample	direct
estimated_library_size	0..1 Float		direct
total_reads	0..1 Float	total number of reads	direct
percent_rRNA	0..1 Float		direct
percent_mRNA	0..1 Float		direct
percent_mtRNA	0..1 Float		direct
percent_Globin	0..1 Float		direct
percent_UMI	0..1 Float		direct
5prime3prime_bias	0..1 Float		direct
percent_GC	0..1 Float		direct
percent_chrX_Y	0..1 Float		direct

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Experiment_rna_short_read
description: Table containing experiment_rna_short_read information
from_schema: https://w3id.org/madanucd/gregor_linkml
slots:
- experiment_rna_short_read_id
- analyte_id
- experiment_sample_id
- seq_library_prep_kit_method
- library_prep_type
- experiment_type
- read_length
- single_or_paired_ends
- date_data_generation
- sequencing_platform
- within_site_batch_name
- RIN
- estimated_library_size
- total_reads
- percent_rRNA
- percent_mRNA
- percent_mtRNA
- percent_Globin
- percent_UMI
- 5prime3prime_bias
- percent_GC
- percent_chrX_Y

Induced

name: Experiment_rna_short_read
description: Table containing experiment_rna_short_read information
from_schema: https://w3id.org/madanucd/gregor_linkml
attributes:
  experiment_rna_short_read_id:
    name: experiment_rna_short_read_id
    description: identifier for experiment
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: experiment_rna_short_read_id
    owner: Experiment_rna_short_read
    domain_of:
    - Experiment_rna_short_read
    - Aligned_rna_short_read
    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_rna_short_read
    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_rna_short_read
    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_rna_short_read
    domain_of:
    - Experiment_dna_short_read
    - Experiment_rna_short_read
    - Experiment_nanopore
    - Experiment_pac_bio
    - Experiment_atac_short_read
    range: string
  library_prep_type:
    name: library_prep_type
    description: type of library prep
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    multivalued: true
    alias: library_prep_type
    owner: Experiment_rna_short_read
    domain_of:
    - Experiment_rna_short_read
    range: Library_prep_typeEnum
  experiment_type:
    name: experiment_type
    description: ''
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: experiment_type
    owner: Experiment_rna_short_read
    domain_of:
    - Experiment_dna_short_read
    - Experiment_rna_short_read
    - Experiment_nanopore
    - Experiment_pac_bio
    - Experiment_atac_short_read
    range: Experiment_typeEnum
    required: true
  read_length:
    name: read_length
    description: sequenced read length (bp); GREGoR RCs do paired end sequencing,
      so is the example of 100bp indicates 2x100bp.
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: read_length
    owner: Experiment_rna_short_read
    domain_of:
    - Experiment_dna_short_read
    - Experiment_rna_short_read
    - Experiment_atac_short_read
    range: integer
  single_or_paired_ends:
    name: single_or_paired_ends
    description: single or paired end
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: single_or_paired_ends
    owner: Experiment_rna_short_read
    domain_of:
    - Experiment_rna_short_read
    range: Single_or_paired_endsEnum
    required: true
  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_rna_short_read
    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_rna_short_read
    domain_of:
    - Experiment_dna_short_read
    - Experiment_rna_short_read
    - Experiment_nanopore
    - Experiment_pac_bio
    - Experiment_atac_short_read
    range: string
  within_site_batch_name:
    name: within_site_batch_name
    description: batch number for the site, important for future batch correction
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: within_site_batch_name
    owner: Experiment_rna_short_read
    domain_of:
    - Experiment_rna_short_read
    range: string
    required: true
  RIN:
    name: RIN
    description: RIN number for quality of sample
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: RIN
    owner: Experiment_rna_short_read
    domain_of:
    - Experiment_rna_short_read
    range: float
  estimated_library_size:
    name: estimated_library_size
    description: ''
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: estimated_library_size
    owner: Experiment_rna_short_read
    domain_of:
    - Experiment_rna_short_read
    range: float
  total_reads:
    name: total_reads
    description: total number of reads
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: total_reads
    owner: Experiment_rna_short_read
    domain_of:
    - Experiment_rna_short_read
    range: float
  percent_rRNA:
    name: percent_rRNA
    description: ''
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: percent_rRNA
    owner: Experiment_rna_short_read
    domain_of:
    - Experiment_rna_short_read
    range: float
  percent_mRNA:
    name: percent_mRNA
    description: ''
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: percent_mRNA
    owner: Experiment_rna_short_read
    domain_of:
    - Experiment_rna_short_read
    range: float
  percent_mtRNA:
    name: percent_mtRNA
    description: ''
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: percent_mtRNA
    owner: Experiment_rna_short_read
    domain_of:
    - Experiment_rna_short_read
    range: float
  percent_Globin:
    name: percent_Globin
    description: ''
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: percent_Globin
    owner: Experiment_rna_short_read
    domain_of:
    - Experiment_rna_short_read
    range: float
  percent_UMI:
    name: percent_UMI
    description: ''
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: percent_UMI
    owner: Experiment_rna_short_read
    domain_of:
    - Experiment_rna_short_read
    range: float
  5prime3prime_bias:
    name: 5prime3prime_bias
    description: ''
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: 5prime3prime_bias
    owner: Experiment_rna_short_read
    domain_of:
    - Experiment_rna_short_read
    range: float
  percent_GC:
    name: percent_GC
    description: ''
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: percent_GC
    owner: Experiment_rna_short_read
    domain_of:
    - Experiment_rna_short_read
    range: float
  percent_chrX_Y:
    name: percent_chrX_Y
    description: ''
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: percent_chrX_Y
    owner: Experiment_rna_short_read
    domain_of:
    - Experiment_rna_short_read
    range: float