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The Next Million Names for Archaea and Bacteria

Mark J. Pallenet al.The Next Million Names for Archaea and Bacteria,Trends in Microbiology (2020).DOI: 10.1016/j.tim.2020.10.009

To generate a large number of new names, we apply a combinatorial approach starting with two or three sets ofcurated roots, that are processed to produce all their possible combinations while keeping trace of their grammatical metadata to draft a valid etymology.

The scripts in this repository require Python (at least 3.6) and these modules:

• itertools (ships with Python)
• pandas (>1.0)
• xlrd (1.2.0)

To run the scripts of this repository, we suggest to create a conda environment as follows:

conda create -c conda-forge -n gan python=3.8 pandas pip ipythonconda activate ganpip install xlrd==1.2.0

A set of two (or three) Excel tables formatted as shown below is used to generate the list of combinations in JSON, HTML and LaTeX format.

Synopsis:

usage: gan-genus.py [-h] -1 FIRST -2 SECOND [-3 THIRD] -o OUTDIR [-p PREFIX] [-c CONNECTOR] [-v]

For full usage and installation instructions, pleasecheck the documentation.

Using three small files in theinput_test directory (8, 11 and 8 words, respectively), GAN produced 968 (8 x 11 x 8)combinations:

• inPDF format
• inHTML format

"The great automatic nomenclaturer" is a reference to a short story ("The Great Automatic Grammatizator")written by the British author Roald Dahl [link].