Gnomic-grammar NPM

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.