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.