Taxonomy¶
This module provides access to the NCBI’s organism taxonomy information and organism name unification across different modules.
Usage¶
The following script takes the list of taxonomy IDs and prints out their name:
from orangecontrib.bioinformatics.ncbi import taxonomy
for taxid in taxonomy.common_taxids():
print(f"{taxid:<10}{taxonomy.name(taxid):<30}{','.join(name for name in taxonomy.shortname(taxid))}")
The output of the script is:
6500 Aplysia californica aplysia
3702 Arabidopsis thaliana arabidopsis,thaliana,plant
9913 Bos taurus cattle,cow
6239 Caenorhabditis elegans nematode,roundworm
5476 Candida albicans thrush,candidiasis,candida
3055 Chlamydomonas reinhardtii algae
7955 Danio rerio zebrafish
44689 Dictyostelium discoideum dicty,amoeba,slime mold
7227 Drosophila melanogaster fly,fruit fly,vinegar fly
562 Escherichia coli ecoli,coli,bacterium
11103 Hepatitis C virus virus, hepatitis
9606 Homo sapiens human
10090 Mus musculus mouse,mus
2104 Mycoplasma pneumoniae bacterium,mycoplasma
4530 Oryza sativa asian rice,rice,cereal,plant
5833 Plasmodium falciparum plasmodium,malaria,parasite
4754 Pneumocystis carinii pneumonia,fungus
10116 Rattus norvegicus rat,laboratory rat
4932 Saccharomyces cerevisiae yeast,baker yeast,brewer yeast
4896 Schizosaccharomyces pombe yeast,fission yeast
31033 Takifugu rubripes fish,pufferfish
8355 Xenopus laevis frog,african clawed frog
4577 Zea mays corn,cereal grain,plant