Bioconductor Custom Annotation Data Package

Description

Welcome to the mirbase.db custom annotation package. This package contains multiple organisms. The purpose is to provide detailed information about the mirRBase microRNA database (http://www.mirbase.org/). In particular, it covers the searchable database of published microRNA sequences and annotation and not the miRBase Registry and Targets database. As requested by the providers of this resource, the references below should be cited when making use of the data. Ambros et al. 2003 provides guidelines on microRNA annotation.

The current version and release date are: miRBase (Version: 19) ftp://mirbase.org/pub/mirbase/CURRENT/ With a date stamp from the source of: 01 Aug 2012. This information is also available by using the mirbase() function.

This package is updated biannually.

You can learn what objects this package supports with the following command: ls("package:mirbase.db")

Each of these objects has their own manual page detailing where relevant data was obtained along with examples of how to use it. Many of these objects also have a reverse map available. When this is true, expect to usually find relevant information on the same manual page as the forward map.

References

Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ. miRBase: tools for microRNA genomics. NAR 2008 36(Database Issue):D154-D158 http://nar.oxfordjournals.org/cgi/content/full/36/suppl_1/D154

Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ. miRBase: microRNA sequences, targets and gene nomenclature. NAR 2006 34(Database Issue):D140-D144 http://nar.oxfordjournals.org/cgi/content/full/34/suppl_1/D140

Griffiths-Jones S. The microRNA Registry. NAR 2004 32(Database Issue):D109-D111 http://nar.oupjournals.org/cgi/content/full/32/suppl_1/D109

Ambros V, Bartel B, Bartel DP, Burge CB, Carrington JC, Chen X, Dreyfuss G, Eddy SR, Griffiths-Jones S, Marshall M, Matzke M, Ruvkun G, Tuschl T. A uniform system for microRNA annotation. RNA 2003 9(3):277-279 http://www.rnajournal.org/cgi/content/full/9/3/277

Examples

  ls("package:mirbase.db")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(mirbase.db)
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/mirbase.db/mirbaseBASE.Rd_%03d_medium.png", width=480, height=480)
> ### Name: mirbase.db
> ### Title: Bioconductor Custom Annotation Data Package
> ### Aliases: mirbase.db mirbase
> ### Keywords: data
> 
> ### ** Examples
> 
>   ls("package:mirbase.db")
 [1] "contextNumber"           "contextOverlapSense"    
 [3] "contextOverlapType"      "contextTranscriptID"    
 [5] "contextTranscriptName"   "contextTranscriptSource"
 [7] "linksDbId"               "linksDbLink"            
 [9] "linksDbSecondary"        "matureAccession"        
[11] "matureEvidence"          "matureExperiment"       
[13] "matureFrom"              "matureName"             
[15] "matureSimilarity"        "matureTo"               
[17] "mirbase"                 "mirbaseACC2ID"          
[19] "mirbaseCHR"              "mirbaseCHRLOC"          
[21] "mirbaseCHRLOCEND"        "mirbaseCLUSTER"         
[23] "mirbaseCOMMENT"          "mirbaseCONTEXT"         
[25] "mirbaseDESCRIPTION"      "mirbaseFAMILY"          
[27] "mirbaseHAIRPIN"          "mirbaseID2ACC"          
[29] "mirbaseID2SPECIES"       "mirbaseLINKS"           
[31] "mirbaseMAPCOUNTS"        "mirbaseMATURE"          
[33] "mirbaseMFE"              "mirbasePMID"            
[35] "mirbaseSEQUENCE"         "mirbaseSPECIES"         
[37] "mirbaseSPECIES2ID"       "mirbase_dbInfo"         
[39] "mirbase_dbconn"          "mirbase_dbfile"         
[41] "mirbase_dbschema"        "pmidAuthor"             
[43] "pmidJournal"             "pmidMedline"            
[45] "pmidOrderAdded"          "pmidTitle"              
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>