AHEnsDbs 1.1.10
Authors: Johannes Rainer
Last modified: 2023-04-26 02:30:15.57957
Compiled: Wed Sep 6 09:07:53 2023
EnsDb databases from AnnotationHubThe AHEnsDbs package provides the metadata for all EnsDb SQLite databases in
AnnotationHub. First we load/update the AnnotationHub resource.
library(AnnotationHub)
ah <- AnnotationHub()Next we list all EnsDb entries from AnnotationHub.
query(ah, "EnsDb")## AnnotationHub with 4319 records
## # snapshotDate(): 2023-04-25
## # $dataprovider: Ensembl
## # $species: Sus scrofa, Mus musculus, Gallus gallus, Rattus norvegicus, Oryz...
## # $rdataclass: EnsDb
## # additional mcols(): taxonomyid, genome, description,
## # coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
## # rdatapath, sourceurl, sourcetype
## # retrieve records with, e.g., 'object[["AH53185"]]'
##
## title
## AH53185 | Ensembl 87 EnsDb for Anolis Carolinensis
## AH53186 | Ensembl 87 EnsDb for Ailuropoda Melanoleuca
## AH53187 | Ensembl 87 EnsDb for Astyanax Mexicanus
## AH53188 | Ensembl 87 EnsDb for Anas Platyrhynchos
## AH53189 | Ensembl 87 EnsDb for Bos Taurus
## ... ...
## AH113851 | Ensembl 110 EnsDb for Xiphophorus maculatus
## AH113852 | Ensembl 110 EnsDb for Xenopus tropicalis
## AH113853 | Ensembl 110 EnsDb for Zonotrichia albicollis
## AH113854 | Ensembl 110 EnsDb for Zalophus californianus
## AH113855 | Ensembl 110 EnsDb for Zosterops lateralis melanopsWe fetch the EnsDb for species Ciona Intestinalis and ensembl release 87.
qr <- query(ah, c("EnsDb", "intestinalis", "87"))
edb <- qr[[1]]## loading from cache## require("ensembldb")To get the genes defined for this species we can simply call.
genes(edb)## GRanges object with 17153 ranges and 7 metadata columns:
## seqnames ranges strand | gene_id
## <Rle> <IRanges> <Rle> | <character>
## ENSCING00000017842 1 1636-1902 + | ENSCING00000017842
## ENSCING00000016550 1 4219-20394 - | ENSCING00000016550
## ENSCING00000016539 1 23518-34155 + | ENSCING00000016539
## ENSCING00000002700 1 37108-60412 - | ENSCING00000002700
## ENSCING00000002712 1 62406-66903 - | ENSCING00000002712
## ... ... ... ... . ...
## ENSCING00000025225 MT 11275-11335 + | ENSCING00000025225
## ENSCING00000025226 MT 11337-12899 + | ENSCING00000025226
## ENSCING00000025227 MT 12910-12973 + | ENSCING00000025227
## ENSCING00000025228 MT 12990-14724 + | ENSCING00000025228
## ENSCING00000025229 MT 14725-14790 + | ENSCING00000025229
## gene_name gene_biotype seq_coord_system
## <character> <character> <character>
## ENSCING00000017842 misc_RNA chromosome
## ENSCING00000016550 protein_coding chromosome
## ENSCING00000016539 protein_coding chromosome
## ENSCING00000002700 protein_coding chromosome
## ENSCING00000002712 protein_coding chromosome
## ... ... ... ...
## ENSCING00000025225 Mt_tRNA chromosome
## ENSCING00000025226 COI protein_coding chromosome
## ENSCING00000025227 Mt_tRNA chromosome
## ENSCING00000025228 NADH5 protein_coding chromosome
## ENSCING00000025229 Mt_tRNA chromosome
## description symbol entrezid
## <character> <character> <list>
## ENSCING00000017842 NULL <NA>
## ENSCING00000016550 NULL <NA>
## ENSCING00000016539 NULL <NA>
## ENSCING00000002700 NULL <NA>
## ENSCING00000002712 NULL 100181294
## ... ... ... ...
## ENSCING00000025225 NULL <NA>
## ENSCING00000025226 cytochrome oxidase s.. COI 806118
## ENSCING00000025227 NULL <NA>
## ENSCING00000025228 NADH dehydrogenase s.. NADH5 806127
## ENSCING00000025229 NULL <NA>
## -------
## seqinfo: 763 sequences (1 circular) from KH genomeThis section describes the (semi)-automated way to create ensembldb EnsDb
SQLite annotation databases using the Ensembl Perl API and the MySQL database
dumps from Ensembl.
EnsDb SQLite databasesTo create the databases we are sequentially downloading and installing the MySQL database dumps from Ensembl locally and query these local databases to extract the annotations that will be inserted into the final SQLite databases. While it would be possible to directly query the Ensembl databases using the Perl API, this has proven to be slower and frequently fails due to access shortages or time outs.
Below we load the ensembldb package and the generate-EnsDbs.R script in its
scripts folder.
library(ensembldb)
scr <- system.file("scripts/generate-EnsDBs.R", package = "ensembldb")
source(scr)We next use the createEnsDbForSpecies function. This function queries first
the Ensembl ftp server to list all species for a certain Ensembl release. By
default it will then process all species, by first downloading the MySQL
database dumps, installing it into a local MySQL server and subsequently, using
functionality from the ensembldb package and the Ensembl Perl API, exctracting
all annotations from it and storing it to a SQLite datababse. The local MySQL
database will then by default deleted (setting the parameter dropDb = FALSE
does not delete the databases).
Important parameter to set in the function are:
+ ftp_folder: by default the main Ensembl ftp server will be queried
(ftp://ftp.ensembl.org/pub), alternatively, also the Ensemblgenomes database
can be queried. To build e.g. EnsDbs for all plants use
ftp://ftp.ensemblgenomes.org/pub/release-34/plants/mysql. If this parameter
is defined it has to point to the directory in which all MySQL database dumps
can be found.
+ ens_version: the Ensembl version (e.g. 87).
+ user: the user name for the local MySQL database.
+ host: the hostname of the local MySQL database (e.g. "localhost").
+ pass: the password for the local MySQL database.
Below we create all EnsDb databases for Ensembl release 87. Note that we have
to have installed the Ensembl Perl API matching this release.
createEnsDbForSpecies(ens_version = 87, user = "someuser", host = "localhost",
pass = "somepass")All SQLite database, one per species, will be stored in the current working directory.