gson

gson provides a lightweight container and exchange format for gene set collections. A GSON object stores gene set membership together with gene set names, gene identifiers, species, version, source, and URL metadata so the same collection can be reused across enrichment analysis and related workflows. The gson format is natively supported by enrichit and the clusterProfiler family of enrichment analysis packages, and can also be used as a general-purpose gene set collection container.

The core table is gsid2gene, a long data frame with one row per gene set-gene membership. Optional tables map gene set IDs to readable names (gsid2name) and gene IDs to readable gene names (gene2name).

Installation

remotes::install_github("YuLab-SMU/gson")

Create a Gene Set Collection

library(gson)

gsid2gene <- data.frame(
    gsid = c("GS1", "GS1", "GS2"),
    gene = c("101", "102", "103")
)

gsid2name <- data.frame(
    gsid = c("GS1", "GS2"),
    name = c("cell cycle", "immune response")
)

x <- gson(
    gsid2gene = gsid2gene,
    gsid2name = gsid2name,
    schema_version = "1.0",
    species = "Homo sapiens",
    gsname = "example",
    version = "2026-06-30",
    keytype = "ENTREZID"
)

x

Read and Write GSON

f <- tempfile(fileext = ".gson")

write.gson(x, f)
y <- read.gson(f)

The .gson file is JSON, so it can be inspected, archived, and passed between tools without an R-specific binary format.

The current GSON schema version is 1.0. New files written by write.gson() include schema_version so future readers can distinguish the file schema from the R package version.

Read GMT

gmt <- system.file(
    "extdata",
    "wikipathways-20220310-gmt-Homo_sapiens.gmt",
    package = "gson"
)

wp <- read.gmt.wp(gmt, output = "GSON")
wp

For generic GMT files, use read.gmt() to obtain a long data frame with term and gene columns, then construct a GSON object after mapping the term column to the gene set identifiers used by your workflow.

Use with Enrichment Analysis

Many enrichment tools need a two-column gene set membership table. A GSON object keeps that table together with the metadata needed to interpret the result:

term2gene <- x@gsid2gene
term2name <- x@gsid2name

Keeping keytype, species, version, and source metadata with the membership table makes enrichment results easier to reproduce and compare.

Data Contract

A .gson file stores the collection as JSON:

{
  "gsid2gene": {"GS1": ["101", "102"]},
  "gsid2name": {"gsid": ["GS1"], "name": ["cell cycle"]},
  "gene2name": null,
  "schema_version": ["1.0"],
  "species": ["Homo sapiens"],
  "gsname": ["example"],
  "version": ["2026-06-30"],
  "accessed_date": null,
  "keytype": ["ENTREZID"],
  "urlpattern": null,
  "info": null
}

A GSON object represents one gene set collection.

• gsid2gene is required and contains gsid and gene.
• gsid2name is optional and contains gsid and name.
• gene2name is optional and contains gene and name.
• schema_version describes the GSON file schema, currently 1.0.
• species, gsname, version, accessed_date, keytype, urlpattern, and info describe the source and interpretation of the collection.