miRBaseVersions.db

A Bioconductor-style annotation R package shipping mature miRNA names from 23 miRBase release versions (6.0 through 22.1). Exposed through the standard AnnotationDbi select interface so it plugs in alongside any other annotation package.

Use it to translate or reconcile mature miRNA accessions and names across miRBase versions — e.g. mapping a legacy MIMAT accession to its current v22.1 name, or pulling the full per-version naming history of a miRNA.

Installation

# install.packages("BiocManager")
BiocManager::install("AnnotationDbi")          # required dependency

# install miRBaseVersions.db from source
# R CMD INSTALL miRBaseVersions.db

Runtime dependencies: AnnotationDbi, DBI, RSQLite, methods, gtools.

Quick start

library(miRBaseVersions.db)

# What can I query?
keytypes(miRBaseVersions.db)
#>  [1] "MIMAT"        "VW-MIMAT-22.1" "VW-MIMAT-22.0" ... "VW-MIMAT-6.0"

columns(miRBaseVersions.db)
#> [1] "ACCESSION" "NAME" "ORGANISM" "SEQUENCE" "VERSION"

# Full naming history of one mature miRNA across every release
select(miRBaseVersions.db,
       keys    = "MIMAT0000092",
       keytype = "MIMAT",
       columns = c("ACCESSION", "NAME", "VERSION"))

# Just the names present in the current release
keys(miRBaseVersions.db, keytype = "VW-MIMAT-22.1")[1:5]

The MIMAT keytype searches across every version. Each VW-MIMAT-<X.Y> keytype is a per-release SQL view that filters down to one version.

Versions covered

miRBase version	Mature entries	Released
6.0	1,591	04/05
7.1	3,101	10/05
8.0	3,228	02/06
8.1	3,684	05/06
8.2	3,834	07/06
9.0	4,167	10/06
9.1	4,274	02/07
9.2	4,430	05/07
10.0	5,395	08/07
10.1	5,718	12/07
11.0	6,703	04/08
12.0	9,110	09/08
13.0	10,097	03/09
14.0	11,663	09/09
15.0	15,632	04/10
16.0	17,341	08/10
17.0	19,724	04/11
18.0	21,643	11/11
19.0	25,141	08/12
20.0	30,424	06/13
21.0	35,828	06/14
22.0	48,885	03/18
22.1	48,885	10/18

277 organisms in total.

Note on v22.1. miRBase 22.1 only updated the high-confidence subset (which this package does not model); sequences, accessions and names are unchanged from v22.0. The VW-MIMAT-22.1 keytype is therefore a relabelled alias view over VW-MIMAT-22.0 rather than a separately ingested release. Querying it yields the same rows as v22.0 with VERSION = 22.1.

Documentation

A worked-examples vignette is included with the package:

vignette("miRBaseVersions.db-vignette")

License

Artistic-2.0