Enum: CommonOrganismTaxaEnum

Common model organisms used in biological research, mapped to NCBI Taxonomy IDs

URI: valuesets:CommonOrganismTaxaEnum

Permissible Values

Value	Meaning	Description
BACTERIA	NCBITaxon:2	Bacteria domain
ARCHAEA	NCBITaxon:2157	Archaea domain
EUKARYOTA	NCBITaxon:2759	Eukaryota domain
VIRUSES	NCBITaxon:10239	Viruses (not a true domain)
VERTEBRATA	NCBITaxon:7742	Vertebrates
MAMMALIA	NCBITaxon:40674	Mammals
PRIMATES	NCBITaxon:9443	Primates
RODENTIA	NCBITaxon:9989	Rodents
CARNIVORA	NCBITaxon:33554	Carnivores
ARTIODACTYLA	NCBITaxon:91561	Even-toed ungulates
AVES	NCBITaxon:8782	Birds
ACTINOPTERYGII	NCBITaxon:7898	Ray-finned fishes
AMPHIBIA	NCBITaxon:8292	Amphibians
ARTHROPODA	NCBITaxon:6656	Arthropods
INSECTA	NCBITaxon:50557	Insects
NEMATODA	NCBITaxon:6231	Roundworms
FUNGI	NCBITaxon:4751	Fungal kingdom
ASCOMYCOTA	NCBITaxon:4890	Sac fungi
VIRIDIPLANTAE	NCBITaxon:33090	Green plants
MAGNOLIOPHYTA	NCBITaxon:3398	Flowering plants
PROTEOBACTERIA	NCBITaxon:1224	Proteobacteria
GAMMAPROTEOBACTERIA	NCBITaxon:1236	Gamma proteobacteria
FIRMICUTES	NCBITaxon:1239	Firmicutes (Gram-positive bacteria)
ACTINOBACTERIA	NCBITaxon:201174	Actinobacteria
EURYARCHAEOTA	NCBITaxon:28890	Euryarchaeota
APICOMPLEXA	NCBITaxon:5794	Apicomplexan parasites
HUMAN	NCBITaxon:9606	Homo sapiens (human)
MOUSE	NCBITaxon:10090	Mus musculus (house mouse)
RAT	NCBITaxon:10116	Rattus norvegicus (Norway rat)
RHESUS	NCBITaxon:9544	Macaca mulatta (rhesus macaque)
CHIMP	NCBITaxon:9598	Pan troglodytes (chimpanzee)
DOG	NCBITaxon:9615	Canis lupus familiaris (dog)
COW	NCBITaxon:9913	Bos taurus (cattle)
PIG	NCBITaxon:9823	Sus scrofa (pig)
CHICKEN	NCBITaxon:9031	Gallus gallus (chicken)
ZEBRAFISH	NCBITaxon:7955	Danio rerio (zebrafish)
MEDAKA	NCBITaxon:8090	Oryzias latipes (Japanese medaka)
PUFFERFISH	NCBITaxon:31033	Takifugu rubripes (torafugu)
XENOPUS_TROPICALIS	NCBITaxon:8364	Xenopus tropicalis (western clawed frog)
XENOPUS_LAEVIS	NCBITaxon:8355	Xenopus laevis (African clawed frog)
DROSOPHILA	NCBITaxon:7227	Drosophila melanogaster (fruit fly)
C_ELEGANS	NCBITaxon:6239	Caenorhabditis elegans (roundworm)
S_CEREVISIAE	NCBITaxon:4932	Saccharomyces cerevisiae (baker's yeast)
S_CEREVISIAE_S288C	NCBITaxon:559292	Saccharomyces cerevisiae S288C (reference strain)
S_POMBE	NCBITaxon:4896	Schizosaccharomyces pombe (fission yeast)
C_ALBICANS	NCBITaxon:5476	Candida albicans (pathogenic yeast)
A_NIDULANS	NCBITaxon:162425	Aspergillus nidulans (filamentous fungus)
N_CRASSA	NCBITaxon:5141	Neurospora crassa (red bread mold)
ARABIDOPSIS	NCBITaxon:3702	Arabidopsis thaliana (thale cress)
RICE	NCBITaxon:4530	Oryza sativa (rice)
MAIZE	NCBITaxon:4577	Zea mays (corn)
TOMATO	NCBITaxon:4081	Solanum lycopersicum (tomato)
TOBACCO	NCBITaxon:4097	Nicotiana tabacum (tobacco)
E_COLI	NCBITaxon:562	Escherichia coli
E_COLI_K12	NCBITaxon:83333	Escherichia coli str
B_SUBTILIS	NCBITaxon:1423	Bacillus subtilis
M_TUBERCULOSIS	NCBITaxon:1773	Mycobacterium tuberculosis
P_AERUGINOSA	NCBITaxon:287	Pseudomonas aeruginosa
S_AUREUS	NCBITaxon:1280	Staphylococcus aureus
S_PNEUMONIAE	NCBITaxon:1313	Streptococcus pneumoniae
H_PYLORI	NCBITaxon:210	Helicobacter pylori
M_JANNASCHII	NCBITaxon:2190	Methanocaldococcus jannaschii
H_SALINARUM	NCBITaxon:2242	Halobacterium salinarum
P_FALCIPARUM	NCBITaxon:5833	Plasmodium falciparum (malaria parasite)
T_GONDII	NCBITaxon:5811	Toxoplasma gondii
T_BRUCEI	NCBITaxon:5691	Trypanosoma brucei
DICTYOSTELIUM	NCBITaxon:44689	Dictyostelium discoideum (slime mold)
TETRAHYMENA	NCBITaxon:5911	Tetrahymena thermophila
PARAMECIUM	NCBITaxon:5888	Paramecium tetraurelia
CHLAMYDOMONAS	NCBITaxon:3055	Chlamydomonas reinhardtii (green alga)
PHAGE_LAMBDA	NCBITaxon:10710	Escherichia phage lambda
HIV1	NCBITaxon:11676	Human immunodeficiency virus 1
INFLUENZA_A	NCBITaxon:11320	Influenza A virus
SARS_COV_2	NCBITaxon:2697049	Severe acute respiratory syndrome coronavirus 2

Slots

Name	Description
common_organism_taxa	Common model organisms used in biological research, mapped to NCBI Taxonomy I...

Identifier and Mapping Information

Schema Source

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

LinkML Source

name: CommonOrganismTaxaEnum
description: Common model organisms used in biological research, mapped to NCBI Taxonomy
  IDs
from_schema: https://w3id.org/linkml/valuesets
rank: 1000
permissible_values:
  BACTERIA:
    text: BACTERIA
    description: Bacteria domain
    meaning: NCBITaxon:2
    instantiates:
    - taxon:Domain
  ARCHAEA:
    text: ARCHAEA
    description: Archaea domain
    meaning: NCBITaxon:2157
  EUKARYOTA:
    text: EUKARYOTA
    description: Eukaryota domain
    meaning: NCBITaxon:2759
  VIRUSES:
    text: VIRUSES
    description: Viruses (not a true domain)
    meaning: NCBITaxon:10239
  VERTEBRATA:
    text: VERTEBRATA
    description: Vertebrates
    meaning: NCBITaxon:7742
    is_a: EUKARYOTA
    title: Vertebrata <vertebrates>
  MAMMALIA:
    text: MAMMALIA
    description: Mammals
    meaning: NCBITaxon:40674
    is_a: VERTEBRATA
  PRIMATES:
    text: PRIMATES
    description: Primates
    meaning: NCBITaxon:9443
    is_a: MAMMALIA
  RODENTIA:
    text: RODENTIA
    description: Rodents
    meaning: NCBITaxon:9989
    is_a: MAMMALIA
  CARNIVORA:
    text: CARNIVORA
    description: Carnivores
    meaning: NCBITaxon:33554
    is_a: MAMMALIA
  ARTIODACTYLA:
    text: ARTIODACTYLA
    description: Even-toed ungulates
    meaning: NCBITaxon:91561
    is_a: MAMMALIA
  AVES:
    text: AVES
    description: Birds
    meaning: NCBITaxon:8782
    is_a: VERTEBRATA
  ACTINOPTERYGII:
    text: ACTINOPTERYGII
    description: Ray-finned fishes
    meaning: NCBITaxon:7898
    is_a: VERTEBRATA
  AMPHIBIA:
    text: AMPHIBIA
    description: Amphibians
    meaning: NCBITaxon:8292
    is_a: VERTEBRATA
  ARTHROPODA:
    text: ARTHROPODA
    description: Arthropods
    meaning: NCBITaxon:6656
    is_a: EUKARYOTA
  INSECTA:
    text: INSECTA
    description: Insects
    meaning: NCBITaxon:50557
    is_a: ARTHROPODA
  NEMATODA:
    text: NEMATODA
    description: Roundworms
    meaning: NCBITaxon:6231
    is_a: EUKARYOTA
  FUNGI:
    text: FUNGI
    description: Fungal kingdom
    meaning: NCBITaxon:4751
    is_a: EUKARYOTA
  ASCOMYCOTA:
    text: ASCOMYCOTA
    description: Sac fungi
    meaning: NCBITaxon:4890
    is_a: FUNGI
  VIRIDIPLANTAE:
    text: VIRIDIPLANTAE
    description: Green plants
    meaning: NCBITaxon:33090
    is_a: EUKARYOTA
  MAGNOLIOPHYTA:
    text: MAGNOLIOPHYTA
    description: Flowering plants
    meaning: NCBITaxon:3398
    is_a: VIRIDIPLANTAE
    title: Magnoliopsida
  PROTEOBACTERIA:
    text: PROTEOBACTERIA
    description: Proteobacteria
    meaning: NCBITaxon:1224
    is_a: BACTERIA
    title: Pseudomonadota
  GAMMAPROTEOBACTERIA:
    text: GAMMAPROTEOBACTERIA
    description: Gamma proteobacteria
    meaning: NCBITaxon:1236
    is_a: PROTEOBACTERIA
  FIRMICUTES:
    text: FIRMICUTES
    description: Firmicutes (Gram-positive bacteria)
    meaning: NCBITaxon:1239
    is_a: BACTERIA
    title: Bacillota
  ACTINOBACTERIA:
    text: ACTINOBACTERIA
    description: Actinobacteria
    meaning: NCBITaxon:201174
    is_a: BACTERIA
    title: Actinomycetota
  EURYARCHAEOTA:
    text: EURYARCHAEOTA
    description: Euryarchaeota
    meaning: NCBITaxon:28890
    is_a: ARCHAEA
    title: Methanobacteriota
  APICOMPLEXA:
    text: APICOMPLEXA
    description: Apicomplexan parasites
    meaning: NCBITaxon:5794
    is_a: EUKARYOTA
  HUMAN:
    text: HUMAN
    description: Homo sapiens (human)
    meaning: NCBITaxon:9606
    is_a: PRIMATES
    title: Homo sapiens
  MOUSE:
    text: MOUSE
    description: Mus musculus (house mouse)
    meaning: NCBITaxon:10090
    is_a: RODENTIA
    title: Mus musculus
  RAT:
    text: RAT
    description: Rattus norvegicus (Norway rat)
    meaning: NCBITaxon:10116
    is_a: RODENTIA
    title: Rattus norvegicus
  RHESUS:
    text: RHESUS
    description: Macaca mulatta (rhesus macaque)
    meaning: NCBITaxon:9544
    is_a: PRIMATES
    title: Macaca mulatta
  CHIMP:
    text: CHIMP
    description: Pan troglodytes (chimpanzee)
    meaning: NCBITaxon:9598
    is_a: PRIMATES
    title: Pan troglodytes
  DOG:
    text: DOG
    description: Canis lupus familiaris (dog)
    meaning: NCBITaxon:9615
    is_a: CARNIVORA
    title: Canis lupus familiaris
  COW:
    text: COW
    description: Bos taurus (cattle)
    meaning: NCBITaxon:9913
    is_a: ARTIODACTYLA
    title: Bos taurus
  PIG:
    text: PIG
    description: Sus scrofa (pig)
    meaning: NCBITaxon:9823
    is_a: ARTIODACTYLA
    title: Sus scrofa
  CHICKEN:
    text: CHICKEN
    description: Gallus gallus (chicken)
    meaning: NCBITaxon:9031
    is_a: AVES
    title: Gallus gallus
  ZEBRAFISH:
    text: ZEBRAFISH
    description: Danio rerio (zebrafish)
    meaning: NCBITaxon:7955
    is_a: ACTINOPTERYGII
    title: Danio rerio
  MEDAKA:
    text: MEDAKA
    description: Oryzias latipes (Japanese medaka)
    meaning: NCBITaxon:8090
    is_a: ACTINOPTERYGII
    title: Oryzias latipes
  PUFFERFISH:
    text: PUFFERFISH
    description: Takifugu rubripes (torafugu)
    meaning: NCBITaxon:31033
    is_a: ACTINOPTERYGII
    title: Takifugu rubripes
  XENOPUS_TROPICALIS:
    text: XENOPUS_TROPICALIS
    description: Xenopus tropicalis (western clawed frog)
    meaning: NCBITaxon:8364
    is_a: AMPHIBIA
  XENOPUS_LAEVIS:
    text: XENOPUS_LAEVIS
    description: Xenopus laevis (African clawed frog)
    meaning: NCBITaxon:8355
    is_a: AMPHIBIA
  DROSOPHILA:
    text: DROSOPHILA
    description: Drosophila melanogaster (fruit fly)
    meaning: NCBITaxon:7227
    is_a: INSECTA
    title: Drosophila melanogaster
  C_ELEGANS:
    text: C_ELEGANS
    description: Caenorhabditis elegans (roundworm)
    meaning: NCBITaxon:6239
    is_a: NEMATODA
    title: Caenorhabditis elegans
  S_CEREVISIAE:
    text: S_CEREVISIAE
    description: Saccharomyces cerevisiae (baker's yeast)
    meaning: NCBITaxon:4932
    is_a: ASCOMYCOTA
    title: Saccharomyces cerevisiae
  S_CEREVISIAE_S288C:
    text: S_CEREVISIAE_S288C
    description: Saccharomyces cerevisiae S288C (reference strain)
    meaning: NCBITaxon:559292
    is_a: S_CEREVISIAE
    title: Saccharomyces cerevisiae S288C
  S_POMBE:
    text: S_POMBE
    description: Schizosaccharomyces pombe (fission yeast)
    meaning: NCBITaxon:4896
    is_a: ASCOMYCOTA
    title: Schizosaccharomyces pombe
  C_ALBICANS:
    text: C_ALBICANS
    description: Candida albicans (pathogenic yeast)
    meaning: NCBITaxon:5476
    is_a: ASCOMYCOTA
    title: Candida albicans
  A_NIDULANS:
    text: A_NIDULANS
    description: Aspergillus nidulans (filamentous fungus)
    meaning: NCBITaxon:162425
    is_a: ASCOMYCOTA
    title: Aspergillus nidulans
  N_CRASSA:
    text: N_CRASSA
    description: Neurospora crassa (red bread mold)
    meaning: NCBITaxon:5141
    is_a: ASCOMYCOTA
    title: Neurospora crassa
  ARABIDOPSIS:
    text: ARABIDOPSIS
    description: Arabidopsis thaliana (thale cress)
    meaning: NCBITaxon:3702
    is_a: MAGNOLIOPHYTA
    title: Arabidopsis thaliana
  RICE:
    text: RICE
    description: Oryza sativa (rice)
    meaning: NCBITaxon:4530
    is_a: MAGNOLIOPHYTA
    title: Oryza sativa
  MAIZE:
    text: MAIZE
    description: Zea mays (corn)
    meaning: NCBITaxon:4577
    is_a: MAGNOLIOPHYTA
    title: Zea mays
  TOMATO:
    text: TOMATO
    description: Solanum lycopersicum (tomato)
    meaning: NCBITaxon:4081
    is_a: MAGNOLIOPHYTA
    title: Solanum lycopersicum
  TOBACCO:
    text: TOBACCO
    description: Nicotiana tabacum (tobacco)
    meaning: NCBITaxon:4097
    is_a: MAGNOLIOPHYTA
    title: Nicotiana tabacum
  E_COLI:
    text: E_COLI
    description: Escherichia coli
    meaning: NCBITaxon:562
    is_a: GAMMAPROTEOBACTERIA
    title: Escherichia coli
  E_COLI_K12:
    text: E_COLI_K12
    description: Escherichia coli str. K-12
    meaning: NCBITaxon:83333
    is_a: E_COLI
    title: Escherichia coli K-12
  B_SUBTILIS:
    text: B_SUBTILIS
    description: Bacillus subtilis
    meaning: NCBITaxon:1423
    is_a: FIRMICUTES
    title: Bacillus subtilis
  M_TUBERCULOSIS:
    text: M_TUBERCULOSIS
    description: Mycobacterium tuberculosis
    meaning: NCBITaxon:1773
    is_a: ACTINOBACTERIA
    title: Mycobacterium tuberculosis
  P_AERUGINOSA:
    text: P_AERUGINOSA
    description: Pseudomonas aeruginosa
    meaning: NCBITaxon:287
    is_a: GAMMAPROTEOBACTERIA
    title: Pseudomonas aeruginosa
  S_AUREUS:
    text: S_AUREUS
    description: Staphylococcus aureus
    meaning: NCBITaxon:1280
    is_a: FIRMICUTES
    title: Staphylococcus aureus
  S_PNEUMONIAE:
    text: S_PNEUMONIAE
    description: Streptococcus pneumoniae
    meaning: NCBITaxon:1313
    is_a: FIRMICUTES
    title: Streptococcus pneumoniae
  H_PYLORI:
    text: H_PYLORI
    description: Helicobacter pylori
    meaning: NCBITaxon:210
    is_a: PROTEOBACTERIA
    title: Helicobacter pylori
  M_JANNASCHII:
    text: M_JANNASCHII
    description: Methanocaldococcus jannaschii
    meaning: NCBITaxon:2190
    is_a: EURYARCHAEOTA
    title: Methanocaldococcus jannaschii
  H_SALINARUM:
    text: H_SALINARUM
    description: Halobacterium salinarum
    meaning: NCBITaxon:2242
    is_a: EURYARCHAEOTA
    title: Halobacterium salinarum
  P_FALCIPARUM:
    text: P_FALCIPARUM
    description: Plasmodium falciparum (malaria parasite)
    meaning: NCBITaxon:5833
    is_a: APICOMPLEXA
    title: Plasmodium falciparum
  T_GONDII:
    text: T_GONDII
    description: Toxoplasma gondii
    meaning: NCBITaxon:5811
    is_a: APICOMPLEXA
    title: Toxoplasma gondii
  T_BRUCEI:
    text: T_BRUCEI
    description: Trypanosoma brucei
    meaning: NCBITaxon:5691
    is_a: EUKARYOTA
    title: Trypanosoma brucei
  DICTYOSTELIUM:
    text: DICTYOSTELIUM
    description: Dictyostelium discoideum (slime mold)
    meaning: NCBITaxon:44689
    is_a: EUKARYOTA
    title: Dictyostelium discoideum
  TETRAHYMENA:
    text: TETRAHYMENA
    description: Tetrahymena thermophila
    meaning: NCBITaxon:5911
    is_a: EUKARYOTA
    title: Tetrahymena thermophila
  PARAMECIUM:
    text: PARAMECIUM
    description: Paramecium tetraurelia
    meaning: NCBITaxon:5888
    is_a: EUKARYOTA
    title: Paramecium tetraurelia
  CHLAMYDOMONAS:
    text: CHLAMYDOMONAS
    description: Chlamydomonas reinhardtii (green alga)
    meaning: NCBITaxon:3055
    is_a: VIRIDIPLANTAE
    title: Chlamydomonas reinhardtii
  PHAGE_LAMBDA:
    text: PHAGE_LAMBDA
    description: Escherichia phage lambda
    meaning: NCBITaxon:10710
    is_a: VIRUSES
    title: Lambdavirus lambda
  HIV1:
    text: HIV1
    description: Human immunodeficiency virus 1
    meaning: NCBITaxon:11676
    is_a: VIRUSES
    title: Human immunodeficiency virus 1
  INFLUENZA_A:
    text: INFLUENZA_A
    description: Influenza A virus
    meaning: NCBITaxon:11320
    is_a: VIRUSES
    title: Influenza A virus
  SARS_COV_2:
    text: SARS_COV_2
    description: Severe acute respiratory syndrome coronavirus 2
    meaning: NCBITaxon:2697049
    is_a: VIRUSES
    title: Severe acute respiratory syndrome coronavirus 2