gnomic-grammar

Gnomic

Gnomic is a grammar for describing genotypes and phenotypes of microbial strains. It is designed to provide an unambiguous, human and machine readable genotype definition notation with flexibility in the level of detail of the definition. The gnomic-grammar NodeJS package contains methods for parsing and analysis of genotype definitions written in gnomic.

Installation

Install the gnomic-grammar package via NPM:

npm install gnomic-grammar

Grammar

The grammar consists of a space- or *comma-*separated list of genotype or phenotype designations described using the following nomenclature:

Designation	Grammar expression
feature deleted	-feature
feature inserted	+feature
site replaced with feature	site>feature
multiple integration site replaced with feature	site>>feature
feature of organism	organism/feature
feature with mutation designation	feature(mutation-designation)
feature with accession number	feature#GB:123456
feature from accession number	#GB:123456
fusion of feature1 and feature2	feature1:feature2
fusion inserted at site using marker	site>fusion::marker+
phenotype: wild-type	phene+ or phene(wild-type)
phenotype: mutant	phene- or phene or phene(mutant)
selection marker: used (wild-type)	marker+
selection marker: available (missing/mutant)	marker-
a non-integrated plasmid	plasmid{} or plasmid{feature, [...]}
plasmid with selection marker	plasmid{feature, [...]}::marker+
integrated vector/plasmid with mandatory integration site	site>vector{feature, [...]}
nucleotide range of a feature	feature[startBase_endBase]
coding nucleotide range of a gene	gene[c.startBase_endBase]
protein amino-acid range of a gene	gene[p.startAA_endAA]
protein amino-acid of a gene	gene[p.AA]
feature of type promoter	promoter.promoterName

Term definitions

Term	Description
gene	a feature that is a gene
feature	a named DNA sequence such as a gene, promoter, or terminator
site	a feature (such as a gene) with a specific location inside the genome of the original strain
phene	an identifier for a feature that comes with a variant definition.
marker	a phenotype important for its role as a selection marker

Examples

Example code	Description
X1>{abcD defG}::M2+, XII2>hijK::M2+, M3-	integrate vector containg abcD and defG at X1 using M1 marker, insert hijK at XII2 using M2 marker, state that M3 marker is available (mutant) in strain
#SGD:YOR202W	insertion of yeast gene 'YOR202W' referenced in the Saccharomyces Genome Database (SGD)
-CAB5#SGD:YDR196C	deletion of yeast gene 'YDR196C' with standard name 'CAB5' referenced in SGD
+E.coli/abcD::Leu2+	insertion of E.coli gene 'abcD' using 'Leu2' selection marker
-abcD	deletion of feature 'abcD' in the parent strain
+abcD::His5+	insertion of feature 'abcD' using the 'His5' selection marker
efgH>abcD	insertion of feature 'abcD' at the location of 'efgH', substituting (deleting) 'efgH'
abcD(cr)	presence of gene 'abcD' with 'cr' (i.e. cold-resistant) mutation
+Pmtr:abcD:Trmt	insertion of the fusion of features 'Pmtr', 'abcD', 'Trmt'
+promoter.Pmtr:abcD:terminator.Trmt	insertion of the fusion of features 'Pmtr', 'abcD', 'Trmt' with explicit types
+abcD:efgH:His5+	insertion of genes 'abcD' and 'efgH' next to each other using the 'His5' selection marker
Abc+	Abc wild-type phenotype
Abc-	Abc mutant phenotype
p123{}	Plasmid p123 present
X1>p123{geneA geneB}::KanMX+	Integration of p123 containing geneA and geneB at X1 using KanMX marker

Contributions

Contributions are very welcome. Please create an issue or contact the author (Lars Schöning) if you would like to propose any significant/breaking changes. Let us know if you want to help us out with a Python version of the grammar.

References

• Wikipedia — Bacterial genetic nomenclature
• Journal of Bacteriology — Instructions to Authors
• Human Genome Variation Society — Recommendations for the description of sequence variants
• Databases cross-referenced in UniProtKB