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Enum: ModelOrganismGenomeBuild

Reference genome assemblies for common model organisms, including all non-human builds used by the Monochrom Ontology. Permissible value names follow the NCBI assembly names (with dots replaced by underscores); UCSC database names are given as aliases.

URI: valuesets:ModelOrganismGenomeBuild

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Permissible Values

Value Title Meaning Description Refseq Accession Taxon Ucsc Name
GRCm39 GRCm39 insdc.gca:GCA_000001635.9 Genome Reference Consortium Mouse Build 39 (Mus musculus), released 2020 GCF_000001635.27 NCBITaxon:10090 mm39
GRCm38 GRCm38 insdc.gca:GCA_000001635.2 Genome Reference Consortium Mouse Build 38 (Mus musculus), released 2011 GCF_000001635.20 NCBITaxon:10090 mm10
mRatBN7_2 mRatBN7.2 insdc.gca:GCA_015227675.2 Rat (Rattus norvegicus) reference assembly mRatBN7.2, released 2020 GCF_015227675.2 NCBITaxon:10116 rn7
Rnor_6_0 Rnor_6.0 insdc.gca:GCA_000001895.4 Rat (Rattus norvegicus) reference assembly Rnor_6.0, released 2014 GCF_000001895.5 NCBITaxon:10116 rn6
GRCz11 GRCz11 insdc.gca:GCA_000002035.4 Genome Reference Consortium Zebrafish Build 11 (Danio rerio), released 2017 GCF_000002035.6 NCBITaxon:7955 danRer11
GRCz10 GRCz10 insdc.gca:GCA_000002035.3 Genome Reference Consortium Zebrafish Build 10 (Danio rerio), released 2014 GCF_000002035.5 NCBITaxon:7955 danRer10
GRCg6a GRCg6a insdc.gca:GCA_000002315.5 Genome Reference Consortium Chicken Build 6a (Gallus gallus), released 2018 GCF_000002315.6 NCBITaxon:9031 galGal6
WBcel235 WBcel235 insdc.gca:GCA_000002985.3 WormBase Caenorhabditis elegans reference assembly WBcel235, released 2013 GCF_000002985.6 NCBITaxon:6239 ce11
BDGP6 Release 6 plus ISO1 MT insdc.gca:GCA_000001215.4 Drosophila melanogaster reference assembly, Release 6 plus ISO1 mitochondrial genome GCF_000001215.4 NCBITaxon:7227 dm6
Callithrix_jacchus_cj1700_1_1 Callithrix_jacchus_cj1700_1.1 insdc.gca:GCA_009663435.2 Common marmoset (Callithrix jacchus) reference assembly cj1700_1.1, released 2019 GCF_009663435.1 NCBITaxon:9483 calJac4

Slots

Name Description
model_organism_genome_build Reference genome build (assembly) for a model organism

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/valuesets

LinkML Source

name: ModelOrganismGenomeBuild
instantiates:
- valuesets_meta:ValueSetEnumDefinition
description: Reference genome assemblies for common model organisms, including all
  non-human builds used by the Monochrom Ontology. Permissible value names follow
  the NCBI assembly names (with dots replaced by underscores); UCSC database names
  are given as aliases.
title: Model Organism Genome Build
from_schema: https://w3id.org/valuesets
contributors:
- orcid:0000-0002-6601-2165
- https://github.com/anthropics/claude-code
status: DRAFT
rank: 1000
permissible_values:
  GRCm39:
    text: GRCm39
    description: Genome Reference Consortium Mouse Build 39 (Mus musculus), released
      2020
    meaning: insdc.gca:GCA_000001635.9
    annotations:
      ucsc_name:
        tag: ucsc_name
        value: mm39
      refseq_accession:
        tag: refseq_accession
        value: GCF_000001635.27
      taxon:
        tag: taxon
        value: NCBITaxon:10090
    title: GRCm39
    aliases:
    - mm39
  GRCm38:
    text: GRCm38
    description: Genome Reference Consortium Mouse Build 38 (Mus musculus), released
      2011
    meaning: insdc.gca:GCA_000001635.2
    annotations:
      ucsc_name:
        tag: ucsc_name
        value: mm10
      refseq_accession:
        tag: refseq_accession
        value: GCF_000001635.20
      taxon:
        tag: taxon
        value: NCBITaxon:10090
    title: GRCm38
    aliases:
    - mm10
  mRatBN7_2:
    text: mRatBN7_2
    description: Rat (Rattus norvegicus) reference assembly mRatBN7.2, released 2020
    meaning: insdc.gca:GCA_015227675.2
    annotations:
      ucsc_name:
        tag: ucsc_name
        value: rn7
      refseq_accession:
        tag: refseq_accession
        value: GCF_015227675.2
      taxon:
        tag: taxon
        value: NCBITaxon:10116
    title: mRatBN7.2
    aliases:
    - rn7
    - mRatBN7.2
  Rnor_6_0:
    text: Rnor_6_0
    description: Rat (Rattus norvegicus) reference assembly Rnor_6.0, released 2014
    meaning: insdc.gca:GCA_000001895.4
    annotations:
      ucsc_name:
        tag: ucsc_name
        value: rn6
      refseq_accession:
        tag: refseq_accession
        value: GCF_000001895.5
      taxon:
        tag: taxon
        value: NCBITaxon:10116
    title: Rnor_6.0
    aliases:
    - rn6
    - Rnor_6.0
  GRCz11:
    text: GRCz11
    description: Genome Reference Consortium Zebrafish Build 11 (Danio rerio), released
      2017
    meaning: insdc.gca:GCA_000002035.4
    annotations:
      ucsc_name:
        tag: ucsc_name
        value: danRer11
      refseq_accession:
        tag: refseq_accession
        value: GCF_000002035.6
      taxon:
        tag: taxon
        value: NCBITaxon:7955
    title: GRCz11
    aliases:
    - danRer11
  GRCz10:
    text: GRCz10
    description: Genome Reference Consortium Zebrafish Build 10 (Danio rerio), released
      2014
    meaning: insdc.gca:GCA_000002035.3
    annotations:
      ucsc_name:
        tag: ucsc_name
        value: danRer10
      refseq_accession:
        tag: refseq_accession
        value: GCF_000002035.5
      taxon:
        tag: taxon
        value: NCBITaxon:7955
    title: GRCz10
    aliases:
    - danRer10
  GRCg6a:
    text: GRCg6a
    description: Genome Reference Consortium Chicken Build 6a (Gallus gallus), released
      2018
    meaning: insdc.gca:GCA_000002315.5
    annotations:
      ucsc_name:
        tag: ucsc_name
        value: galGal6
      refseq_accession:
        tag: refseq_accession
        value: GCF_000002315.6
      taxon:
        tag: taxon
        value: NCBITaxon:9031
    title: GRCg6a
    aliases:
    - galGal6
  WBcel235:
    text: WBcel235
    description: WormBase Caenorhabditis elegans reference assembly WBcel235, released
      2013
    meaning: insdc.gca:GCA_000002985.3
    annotations:
      ucsc_name:
        tag: ucsc_name
        value: ce11
      refseq_accession:
        tag: refseq_accession
        value: GCF_000002985.6
      taxon:
        tag: taxon
        value: NCBITaxon:6239
    title: WBcel235
    aliases:
    - ce11
  BDGP6:
    text: BDGP6
    description: Drosophila melanogaster reference assembly, Release 6 plus ISO1 mitochondrial
      genome
    meaning: insdc.gca:GCA_000001215.4
    annotations:
      ucsc_name:
        tag: ucsc_name
        value: dm6
      refseq_accession:
        tag: refseq_accession
        value: GCF_000001215.4
      taxon:
        tag: taxon
        value: NCBITaxon:7227
    title: Release 6 plus ISO1 MT
    aliases:
    - dm6
    - Release 6 plus ISO1 MT
  Callithrix_jacchus_cj1700_1_1:
    text: Callithrix_jacchus_cj1700_1_1
    description: Common marmoset (Callithrix jacchus) reference assembly cj1700_1.1,
      released 2019
    meaning: insdc.gca:GCA_009663435.2
    annotations:
      ucsc_name:
        tag: ucsc_name
        value: calJac4
      refseq_accession:
        tag: refseq_accession
        value: GCF_009663435.1
      taxon:
        tag: taxon
        value: NCBITaxon:9483
    title: Callithrix_jacchus_cj1700_1.1
    aliases:
    - calJac4
    - Callithrix_jacchus_cj1700_1.1