======== Taxonomy ======== .. py:currentmodule:: orangecontrib.bioinformatics.ncbi.taxonomy This module provides access to the `NCBI's organism taxonomy information `_ and organism name unification across different modules. .. autofunction:: name .. autofunction:: other_names .. autofunction:: search .. autofunction:: lineage .. autofunction:: common_taxids .. autofunction:: common_taxid_to_name Usage ===== The following script takes the list of taxonomy IDs and prints out their name: .. code-block:: python3 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