Class: Sample

Links genomes to NCBI BioProject and BioSample accessions. Enables finding related genomes from same study or sample source.

URI: https://w3id.org/kbase/kbase_ke_pangenome/Sample

classDiagram class Sample click Sample href "../Sample/" Sample : genome_id Sample --> "0..1" Genome : genome_id click Genome href "../Genome/" Sample : ncbi_bioproject_accession_id Sample : ncbi_biosample_accession_id

Slots

Name	Cardinality and Range	Description	Inheritance
genome_id	0..1 Genome	Genome associated with this sample	direct
ncbi_bioproject_accession_id	0..1 String	NCBI BioProject accession	direct
ncbi_biosample_accession_id	0..1 String	NCBI BioSample accession with sample metadata	direct

Identifier and Mapping Information

Annotations

property	value
source_table	sample

Schema Source

from schema: https://w3id.org/kbase/kbase_ke_pangenome

Mappings

Mapping Type	Mapped Value
self	https://w3id.org/kbase/kbase_ke_pangenome/Sample
native	https://w3id.org/kbase/kbase_ke_pangenome/Sample

LinkML Source

Direct

name: Sample
annotations:
  source_table:
    tag: source_table
    value: sample
description: Links genomes to NCBI BioProject and BioSample accessions. Enables finding
  related genomes from same study or sample source.
from_schema: https://w3id.org/kbase/kbase_ke_pangenome
attributes:
  genome_id:
    name: genome_id
    description: Genome associated with this sample
    comments:
    - 'Foreign key: Genome.genome_id'
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    domain_of:
    - Genome
    - Gene
    - GtdbTaxonomyR214v1
    - Sample
    - GapmindPathways
    range: Genome
  ncbi_bioproject_accession_id:
    name: ncbi_bioproject_accession_id
    description: NCBI BioProject accession. Groups related genomes from same study.
    examples:
    - value: PRJNA224116
      description: RefSeq reference genomes project
    - value: PRJNA13883
      description: Human microbiome project
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    domain_of:
    - Sample
    range: string
    pattern: PRJ[A-Z]{2}\d+
  ncbi_biosample_accession_id:
    name: ncbi_biosample_accession_id
    description: NCBI BioSample accession with sample metadata
    examples:
    - value: SAMN02603679
    - value: SAMEA2272191
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    domain_of:
    - Sample
    range: string
    pattern: SAM[NED][A-Z]?\d+

Induced

name: Sample
annotations:
  source_table:
    tag: source_table
    value: sample
description: Links genomes to NCBI BioProject and BioSample accessions. Enables finding
  related genomes from same study or sample source.
from_schema: https://w3id.org/kbase/kbase_ke_pangenome
attributes:
  genome_id:
    name: genome_id
    description: Genome associated with this sample
    comments:
    - 'Foreign key: Genome.genome_id'
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    alias: genome_id
    owner: Sample
    domain_of:
    - Genome
    - Gene
    - GtdbTaxonomyR214v1
    - Sample
    - GapmindPathways
    range: Genome
  ncbi_bioproject_accession_id:
    name: ncbi_bioproject_accession_id
    description: NCBI BioProject accession. Groups related genomes from same study.
    examples:
    - value: PRJNA224116
      description: RefSeq reference genomes project
    - value: PRJNA13883
      description: Human microbiome project
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    alias: ncbi_bioproject_accession_id
    owner: Sample
    domain_of:
    - Sample
    range: string
    pattern: PRJ[A-Z]{2}\d+
  ncbi_biosample_accession_id:
    name: ncbi_biosample_accession_id
    description: NCBI BioSample accession with sample metadata
    examples:
    - value: SAMN02603679
    - value: SAMEA2272191
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    alias: ncbi_biosample_accession_id
    owner: Sample
    domain_of:
    - Sample
    range: string
    pattern: SAM[NED][A-Z]?\d+