Class: LibrarySampleInfo

Information about a specific amplification and sequencing of a specimen

URI: portable_microhaplotype_object:LibrarySampleInfo

classDiagram class LibrarySampleInfo click LibrarySampleInfo href "../LibrarySampleInfo" LibrarySampleInfo : fastqs_loc LibrarySampleInfo : library_prep_plate_info LibrarySampleInfo --> "0..1" PlateInfo : library_prep_plate_info click PlateInfo href "../PlateInfo" LibrarySampleInfo : library_sample_name LibrarySampleInfo : panel_id LibrarySampleInfo : qpcr_parasite_density_info LibrarySampleInfo --> "*" ParasiteDensity : qpcr_parasite_density_info click ParasiteDensity href "../ParasiteDensity" LibrarySampleInfo : run_accession LibrarySampleInfo : sequencing_info_id LibrarySampleInfo : specimen_id

Slots

Name	Cardinality and Range	Description	Inheritance
sequencing_info_id	1 Integer	the index into the sequencing_info list	direct
specimen_id	1 Integer	the index into the specimen_info list	direct
panel_id	1 Integer	the index into the panel_info list	direct
fastqs_loc	0..1 String	the location (url or filename path) of the fastqs for a library run	direct
run_accession	0..1 String	ERA/SRA run accession number for the sample if it was submitted	direct
library_sample_name	1 String	a unique identifier for this sequence/amplification run on a specimen_name	direct
library_prep_plate_info	0..1 PlateInfo	plate location of where library was prepared for sequencing	direct
qpcr_parasite_density_info	* ParasiteDensity	qpcr parasite density measurement	direct

Usages

used by	used in	type	used
PortableMicrohaplotypeObject	library_info	range	LibrarySampleInfo

Identifier and Mapping Information

Schema Source

from schema: https://plasmogenepi.github.io/portable-microhaplotype-object

Mappings

Mapping Type	Mapped Value
self	portable_microhaplotype_object:LibrarySampleInfo
native	portable_microhaplotype_object:LibrarySampleInfo

LinkML Source

Direct

name: LibrarySampleInfo
description: Information about a specific amplification and sequencing of a specimen
from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
slots:
- sequencing_info_id
- specimen_id
- panel_id
slot_usage:
  specimen_id:
    name: specimen_id
    identifier: false
attributes:
  fastqs_loc:
    name: fastqs_loc
    description: the location (url or filename path) of the fastqs for a library run
    examples:
    - value: ftp.sra.ebi.ac.uk/vol1/fastq/SRR332/035/SRR33216235/SRR33216235_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR332/035/SRR33216235/SRR33216235_2.fastq.gz
    - value: MACHINE@/path/to/SRR33216235_1.fastq.gz;MACHINE@/path/to/SRR33216235_2.fastq.gz
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - LibrarySampleInfo
    range: string
    required: false
    pattern: ^[A-z-.;,_0-9\(\),\/\ ]+$
  run_accession:
    name: run_accession
    description: ERA/SRA run accession number for the sample if it was submitted
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - LibrarySampleInfo
    range: string
    required: false
    pattern: ^[A-z-._0-9]+$
  library_sample_name:
    name: library_sample_name
    description: a unique identifier for this sequence/amplification run on a specimen_name
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    identifier: true
    domain_of:
    - LibrarySampleInfo
    range: string
    required: true
    pattern: ^[A-z-._0-9 ]+$
  library_prep_plate_info:
    name: library_prep_plate_info
    description: 'plate location of where library was prepared for sequencing '
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - LibrarySampleInfo
    range: PlateInfo
    required: false
  qpcr_parasite_density_info:
    name: qpcr_parasite_density_info
    description: 'qpcr parasite density measurement '
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - LibrarySampleInfo
    range: ParasiteDensity
    required: false
    multivalued: true
    inlined: true
    inlined_as_list: true

Induced

name: LibrarySampleInfo
description: Information about a specific amplification and sequencing of a specimen
from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
slot_usage:
  specimen_id:
    name: specimen_id
    identifier: false
attributes:
  fastqs_loc:
    name: fastqs_loc
    description: the location (url or filename path) of the fastqs for a library run
    examples:
    - value: ftp.sra.ebi.ac.uk/vol1/fastq/SRR332/035/SRR33216235/SRR33216235_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR332/035/SRR33216235/SRR33216235_2.fastq.gz
    - value: MACHINE@/path/to/SRR33216235_1.fastq.gz;MACHINE@/path/to/SRR33216235_2.fastq.gz
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: fastqs_loc
    owner: LibrarySampleInfo
    domain_of:
    - LibrarySampleInfo
    range: string
    required: false
    pattern: ^[A-z-.;,_0-9\(\),\/\ ]+$
  run_accession:
    name: run_accession
    description: ERA/SRA run accession number for the sample if it was submitted
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: run_accession
    owner: LibrarySampleInfo
    domain_of:
    - LibrarySampleInfo
    range: string
    required: false
    pattern: ^[A-z-._0-9]+$
  library_sample_name:
    name: library_sample_name
    description: a unique identifier for this sequence/amplification run on a specimen_name
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    identifier: true
    alias: library_sample_name
    owner: LibrarySampleInfo
    domain_of:
    - LibrarySampleInfo
    range: string
    required: true
    pattern: ^[A-z-._0-9 ]+$
  library_prep_plate_info:
    name: library_prep_plate_info
    description: 'plate location of where library was prepared for sequencing '
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: library_prep_plate_info
    owner: LibrarySampleInfo
    domain_of:
    - LibrarySampleInfo
    range: PlateInfo
    required: false
  qpcr_parasite_density_info:
    name: qpcr_parasite_density_info
    description: 'qpcr parasite density measurement '
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: qpcr_parasite_density_info
    owner: LibrarySampleInfo
    domain_of:
    - LibrarySampleInfo
    range: ParasiteDensity
    required: false
    multivalued: true
    inlined: true
    inlined_as_list: true
  sequencing_info_id:
    name: sequencing_info_id
    description: the index into the sequencing_info list
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: sequencing_info_id
    owner: LibrarySampleInfo
    domain_of:
    - LibrarySampleInfo
    range: integer
    required: true
    pattern: ^[0-9]+$
  specimen_id:
    name: specimen_id
    description: the index into the specimen_info list
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    identifier: false
    alias: specimen_id
    owner: LibrarySampleInfo
    domain_of:
    - LibrarySampleInfo
    range: integer
    required: true
    pattern: ^[0-9]+$
  panel_id:
    name: panel_id
    description: the index into the panel_info list
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: panel_id
    owner: LibrarySampleInfo
    domain_of:
    - LibrarySampleInfo
    range: integer
    required: true
    pattern: ^[0-9]+$