Gnomic is a human– and computer–readable representation of microbial genotypes and phenotypes. The gnomic Python package contains a parser for the Gnomic grammar able to interpret changes over multiple generations.

The first formal guidelines for microbial genetic nomenclature were drawn up in the 1960s. These traditional nomenclatures are too ambiguous to be useful for modern computer-assisted genome engineering. The gnomic grammar is an improvement over existing nomenclatures, designed to be clear, unambiguous, computer–readable and describe genotypes at various levels of detail.

pip install gnomic

The grammar consists of a list of genotype or phenotype designations, separated by spaces and/or commas. The designations are described using the following nomenclature:

Features may have one or more variants, separated by colon ";" or comma ",".

For example: geneX(cold-resistant; heat-resistant)

Variants can either be identifiers (using the characters a-z, 0-9, "-" and "_") or be sequence variants following the HGVS Sequence Variant Nomenclature.

For example: geneY(c.123G>T)

In this example, we parse "EcGeneA ΔsiteA::promoterB:EcGeneB ΔgeneC" and "ΔgeneA" in gnomic syntax:

>>> from gnomic import Genotype
>>> g1 = Genotype.parse('+Ec/geneA(variant) siteA>P.promoterB:Ec/geneB -geneC')
>>> g1.added_features
{Feature(organism='Ec', name='geneA', variant=('variant',)),
 Feature(organism='Ec', name='geneB'),
 Feature(type='P', name='promoterB')}
>>> g1.removed_features
{Feature(name='geneC'),
 Feature(name='siteA')}

>>> g2 = Genotype.parse('-geneA', parent=g1)
>>> g2.added_features
{Feature(type='P', name='promoterB'),
 Feature(name='geneB', organism='Ec')}
>>> g2.removed_features
{Feature(name='siteA'),
 Feature(name='geneC')}
 >>> g2.changes()
 (Change(multiple=False,
         after=Fusion(annotations=(Feature(type='P', name='promoterB'), Feature(organism='Ec', name='geneB'))),
         before=Feature(name='siteA')),
  Change(multiple=False, before=Feature(name='geneC')))

 >>> g2.format()
 'ΔsiteA→P.promoterB:Ec/geneB ΔgeneC'

To rebuild the gnomic parser using grako (version 3.18.1), run:

grako gnomic-grammar/genotype.enbf -o gnomic/grammar.py -m Gnomic

• Wikipedia — Bacterial genetic nomenclature
• Journal of Bacteriology — Instructions to Authors
• Human Genome Variation Society — Sequence Variant Nomenclature
• Databases cross-referenced in UniProtKB
• MIRIAM Registry