Taxonomy

This module provides access to the NCBI’s organism taxonomy information and organism name unification across different modules.

name(tax_id)

Return the scientific name for organism with provided taxonomy id.

Parameters

tax_id (str) – Taxonomy if (NCBI taxonomy database)

other_names(tax_id)

Return a list of (name, name_type) tuples excluding the scientific name.

Use name to retrieve the scientific name.

Parameters

tax_id (str) – Taxonomy if (NCBI taxonomy database)

search(string, only_species=True, exact=False)

Search the NCBI taxonomy database for an organism.

Parameters

• string (str) – Search string.

• only_species (bool) – Return only taxids of species (and subspecies).

• exact (bool) – Return only taxids of organism that exactly match the string.

lineage(tax_id)

Return a list of taxids ordered from the topmost node (root) to taxid.

Parameters

tax_id (str) – Taxonomy if (NCBI taxonomy database)

common_taxids()

Return taxonomy IDs for most common organisms.

Return type

list of common organisms

common_taxid_to_name(tax_id)

Return a name for a common organism taxonomy id.

Parameters

tax_id (str) – Taxonomy if (NCBI taxonomy database)

Return type

str

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