Organism Taxonomy (taxonomy)

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

orangecontrib.bio.taxonomy.name(taxid)

orangecontrib.bio.taxonomy.other_names(taxid)

orangecontrib.bio.taxonomy.search(string, onlySpecies=True, exact=False)

orangecontrib.bio.taxonomy.lineage(taxid)

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

orangecontrib.bio.taxonomy.taxids()

Returns a list of all (about half a million!) NCBI’s taxonomy ID’s.

orangecontrib.bio.taxonomy.common_taxids()

Return taxonomy IDs for common organisms.

orangecontrib.bio.taxonomy.essential_taxids()

Return taxonomy IDs for organisms that are included in (default) Orange Bioinformatics installation.

Examples

The following script takes the list of taxonomy IDs and prints out their name:

import orangecontrib.bio.taxonomy

for taxid in orangecontrib.bio.taxonomy.common_taxids():
    print("%-6s %s" % (taxid, orangecontrib.bio.taxonomy.name(taxid)))

The output of the script is:

3702   Arabidopsis thaliana
9913   Bos taurus
6239   Caenorhabditis elegans
3055   Chlamydomonas reinhardtii
7955   Danio rerio
352472 Dictyostelium discoideum AX4
7227   Drosophila melanogaster
562    Escherichia coli
11103  Hepatitis C virus
9606   Homo sapiens
10090  Mus musculus
2104   Mycoplasma pneumoniae
4530   Oryza sativa
5833   Plasmodium falciparum
4754   Pneumocystis carinii
10116  Rattus norvegicus
4932   Saccharomyces cerevisiae
4896   Schizosaccharomyces pombe
31033  Takifugu rubripes
8355   Xenopus laevis
4577   Zea mays