Slot: Reference Genome (reference_genome)

Genome record to use as a reference for read alignment or assembly scaffolding. Preferred formats are IMG taxon OID, Mycocosm/Phycocosm/ Phytozome ID, or NCBI assembly accession (GCF/GCA_). Free-text._

URI: nmdc_sub_schema:reference_genome Alias: reference_genome

Applicable Classes

Name	Description	Modifies Slot
JgiIsolateTranscriptomeInterface	JGI submission metadata for isolate TRANSCRIPTOME sequencing projects	no
JgiIsolateCommonMixin	Shared JGI isolate submission fields common to both the genome and the transc...	yes
JgiIsolateGenomeInterface	JGI submission metadata for isolate GENOME sequencing projects	no

Properties

Range: String

Examples

Value
2648501807
GCF_000195995.2
Mycocosm:Aspni7

Comments

Provide a reference if one exists; helps JGI with assembly and QC even for de novo projects.

Identifier and Mapping Information

Schema Source

from schema: https://example.com/nmdc_submission_schema

Mappings

Mapping Type	Mapped Value
self	nmdc_sub_schema:reference_genome
native	nmdc_sub_schema:reference_genome

LinkML Source

name: reference_genome
description: Genome record to use as a reference for read alignment or assembly scaffolding.
  Preferred formats are IMG taxon OID, Mycocosm/Phycocosm/ Phytozome ID, or NCBI assembly
  accession (GCF_/GCA_). Free-text.
title: Reference Genome
notes:
- Local slot pending promotion to nmdc-schema; see https://github.com/microbiomedata/submission-schema/issues/447
comments:
- Provide a reference if one exists; helps JGI with assembly and QC even for de novo
  projects.
examples:
- value: '2648501807'
  description: IMG taxon OID
- value: GCF_000195995.2
  description: NCBI RefSeq assembly accession
- value: Mycocosm:Aspni7
  description: Mycocosm ID
from_schema: https://example.com/nmdc_submission_schema
structured_aliases:
  Reference Genome:
    literal_form: Reference Genome
    predicate: EXACT_SYNONYM
    notes:
    - Exact JGI form template is access-restricted; source is the public submission
      overview.
    source: https://jgi.doe.gov/user-programs/pmo-overview/project-materials-submission-overview/
rank: 40
alias: reference_genome
domain_of:
- JgiIsolateCommonMixin
range: string