The goal of glydb is to provide a comprehensive database of glycan structures, including common glycan structures and their modifications. The database is updated periodically and is used by the glycoverse ecosystem. Only fully defined glycan structures are included.
Installation
The glydb package is not a core glycoverse package. You need to install it individually even if you have installed the meta-package glycoverse.
You can install the latest release of glydb from r-universe (recommended):
# install.packages("pak")
pak::repo_add(glycoverse = "https://glycoverse.r-universe.dev")
pak::pkg_install("glydb")Or from GitHub:
pak::pkg_install("glycoverse/glydb@*release")Or install the development version (NOT recommended):
pak::pkg_install("glycoverse/glydb")Note: Tips and troubleshooting for the meta-package glycoverse are also applicable here: Installation of glycoverse.
Role in glycoverse
The main purpose of glydb is to provide “databases” for the glyanno package. It is also useful for users who want to systematically analyze glycan structures in the database.
Example
Get all data from glydb:
library(glydb)
glydb_data
#> # A tibble: 7,074 × 6
#> glytoucan_ac glycan_structure glycan_composition species confidence
#> <chr> <struct> <comp> <chr> <dbl>
#> 1 G00024MO Glc(b1-3)Glc(b1-3)Glc(b1- Glc(3) Saccha… -1
#> 2 G00025MO Glc(b1-4)Glc(b1-4)Glc(b1-… Glc(4) <NA> -1
#> 3 G00027MO Man(a1-3)[Man(a1-6)]Man(b… Man(3)GlcNAc(1) Mus mu… 0
#> 4 G00030VN Fuc(a1-2)[GalNAc(a1-3)]Ga… Gal(1)GlcNAc(1)Ga… Bos ta… 0
#> 5 G00031MO Gal(b1-3)GalNAc(a1- Gal(1)GalNAc(1) Bos ta… 5.16
#> 6 G00033MO Gal(b1-3)[GlcNAc(b1-6)]Ga… Gal(1)GlcNAc(1)Ga… Bos ta… 3.33
#> 7 G00035MO GlcNAc(b1-3)GalNAc(a1- GlcNAc(1)GalNAc(1) Bos ta… 2.64
#> 8 G00037MO GlcNAc(b1-3)[GlcNAc(b1-6)… GlcNAc(2)GalNAc(1) Bos ta… 1.10
#> 9 G00039MO GalNAc(a1-3)GalNAc(a1- GalNAc(2) Bos ta… 1.61
#> 10 G00041MO GlcNAc(b1-6)GalNAc(a1- GlcNAc(1)GalNAc(1) Bos ta… 1.10
#> # ℹ 7,064 more rows
#> # ℹ 1 more variable: glycan_type <fct>Or use the getter functions to get specific data:
glydb_compositions(mono_type = "generic")
#> <glycan_composition[652]>
#> [1] Hex(3)
#> [2] Hex(4)
#> [3] Hex(3)HexNAc(1)
#> [4] Hex(1)HexNAc(3)dHex(1)NeuGc(1)
#> [5] Hex(1)HexNAc(1)
#> [6] Hex(1)HexNAc(2)
#> [7] HexNAc(2)
#> [8] HexNAc(3)
#> [9] Hex(1)HexNAc(1)dHex(2)
#> [10] Hex(3)HexNAc(1)dHex(1)
#> ... (642 more not shown)
glydb_structures(structure_level = "topological", species = "Homo sapiens", glycan_type = "N")
#> <glycan_structure[289]>
#> [1] GlcNAc(??-?)[GlcNAc(??-?)]Man(??-?)[GlcNAc(??-?)[GlcNAc(??-?)]Man(??-?)]Man(??-?)GlcNAc(??-?)[Fuc(??-?)]GlcNAc(??-
#> [2] Gal(??-?)[Fuc(??-?)]GlcNAc(??-?)Man(??-?)Man(??-?)GlcNAc(??-?)[Fuc(??-?)]GlcNAc(??-
#> [3] Man(??-?)Man(??-?)Man(??-?)[Man(??-?)Man(??-?)]Man(??-?)GlcNAc(??-?)GlcNAc(??-
#> [4] Man(??-?)Man(??-?)GlcNAc(??-?)[Fuc(??-?)]GlcNAc(??-
#> [5] Neu5Ac(??-?)Gal(??-?)GlcNAc(??-?)[Neu5Ac(??-?)Gal(??-?)GlcNAc(??-?)]Man(??-?)[Gal(??-?)GlcNAc(??-?)Man(??-?)]Man(??-?)GlcNAc(??-?)GlcNAc(??-
#> [6] GlcNAc(??-?)Man(??-?)Man(??-?)GlcNAc(??-?)GlcNAc(??-
#> [7] GlcNAc(??-?)[GlcNAc(??-?)]Man(??-?)[GlcNAc(??-?)[GlcNAc(??-?)]Man(??-?)][GlcNAc(??-?)]Man(??-?)GlcNAc(??-?)[Fuc(??-?)]GlcNAc(??-
#> [8] Neu5Ac(??-?)Gal(??-?)GlcNAc(??-?)Gal(??-?)GlcNAc(??-?)[Neu5Ac(??-?)Gal(??-?)GlcNAc(??-?)]Man(??-?)[Neu5Ac(??-?)Gal(??-?)GlcNAc(??-?)[Neu5Ac(??-?)Gal(??-?)GlcNAc(??-?)]Man(??-?)]Man(??-?)GlcNAc(??-?)[Fuc(??-?)]GlcNAc(??-
#> [9] Man(??-?)Man(??-?)[Man(??-?)]Man(??-?)GlcNAc(??-?)GlcNAc(??-
#> [10] Neu5Ac(??-?)Gal(??-?)GlcNAc(??-?)Man(??-?)[Neu5Ac(??-?)Gal(??-?)GlcNAc(??-?)[Neu5Ac(??-?)Gal(??-?)GlcNAc(??-?)]Man(??-?)]Man(??-?)GlcNAc(??-?)GlcNAc(??-
#> ... (279 more not shown)
#> # Unique structures: 289