lehwark / gbson

A new annotation file format based on JSON, containing all information stored in the GenBank format but with advantageoius parsing and information structure properties.

GBSON

File format definition used by the GeSeq annotation software to represent GenBank data as JSON.

Example JSON output

An example output can be found here: GBSON-Example.json.

Usage

To use GBSON in your application you can use any standard JSON parser. If you are programming in JavaScript, just do

const data = JSON.parse(gbson);

In TypeScript you should add the type declaration from this repository to get full IDE support

import { GBSON } from "./GBSON";

const data:GBSON = JSON.parse(gbson);

And access the data like this

const gene = data.features[0].gene;

Range definitions

GenBank

complement(join(125294..125832,126877..127429))

GBSON

{ "complement" : { "joined" : [ [ 125294, 125832 ], [ 126877, 127429 ] ] } }

Nested Features

An advantage of using JSON over GenBank or GFF is its intrinsic capability to express nested structures: