Could you provide a little detail about what you were trying to accomplish and what type of file or output you expected?
The AnnotationHub::query() function only queries AnnotationHub Resources in Bioconductor; It is not an interactive query with web based hosts.
The query you provided is too specific as it queries information about the Resource but not the resource itself which is why adding "CTCF" produced no results. There are currently 10 resources related to "ENCODE" and "Mus Musculus"/"mm9" as shown by using your query without "CTCF"
> hub = AnnotationHub()
snapshotDate(): 2017-09-07
> mm = query(hub, c("ENCODE", "Mus Musculus", "mm9"))
> length(mm)
[1] 10
> mm
AnnotationHub with 10 records
# snapshotDate(): 2017-09-07
# $dataprovider: UCSC
# $species: Mus musculus
# $rdataclass: GRanges
# additional mcols(): taxonomyid, genome, description,
# coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
# rdatapath, sourceurl, sourcetype
# retrieve records with, e.g., 'object[["AH6119"]]'
title
AH6119 | Caltech Histone
AH6120 | Caltech TFBS
AH6121 | LICR Histone
AH6122 | NHGRI BiP
AH6123 | PSU DNaseI HS
AH6124 | PSU Histone
AH6125 | PSU TFBS
AH6126 | Stan/Yale Histone
AH6128 | UW DNaseI DGF
AH6129 | UW DNaseI HS
>
You can get further information about these resources by looking at mcols provided in AnnotationHub.
> names(mcols(mm))
[1] "title" "dataprovider" "species"
[4] "taxonomyid" "genome" "description"
[7] "coordinate_1_based" "maintainer" "rdatadateadded"
[10] "preparerclass" "tags" "rdataclass"
[13] "rdatapath" "sourceurl" "sourcetype"
>
>
> mm$description
[1] "GRanges object from UCSC track 'Caltech Histone'"
[2] "GRanges object from UCSC track 'Caltech TFBS'"
[3] "GRanges object from UCSC track 'LICR Histone'"
[4] "GRanges object from UCSC track 'NHGRI BiP'"
[5] "GRanges object from UCSC track 'PSU DNaseI HS'"
[6] "GRanges object from UCSC track 'PSU Histone'"
[7] "GRanges object from UCSC track 'PSU TFBS'"
[8] "GRanges object from UCSC track 'Stan/Yale Histone'"
[9] "GRanges object from UCSC track 'UW DNaseI DGF'"
[10] "GRanges object from UCSC track 'UW DNaseI HS'"
> mm$sourceurl
[1] "rtracklayer://hgdownload.cse.ucsc.edu/goldenpath/mm9/database/wgEncodeCaltechHist"
[2] "rtracklayer://hgdownload.cse.ucsc.edu/goldenpath/mm9/database/wgEncodeCaltechTfbs"
[3] "rtracklayer://hgdownload.cse.ucsc.edu/goldenpath/mm9/database/wgEncodeLicrHistone"
[4] "rtracklayer://hgdownload.cse.ucsc.edu/goldenpath/mm9/database/wgEncodeNhgriBip"
[5] "rtracklayer://hgdownload.cse.ucsc.edu/goldenpath/mm9/database/wgEncodePsuDnase"
[6] "rtracklayer://hgdownload.cse.ucsc.edu/goldenpath/mm9/database/wgEncodePsuHistone"
[7] "rtracklayer://hgdownload.cse.ucsc.edu/goldenpath/mm9/database/wgEncodePsuTfbs"
[8] "rtracklayer://hgdownload.cse.ucsc.edu/goldenpath/mm9/database/wgEncodeSydhHist"
[9] "rtracklayer://hgdownload.cse.ucsc.edu/goldenpath/mm9/database/wgEncodeUwDgf"
[10] "rtracklayer://hgdownload.cse.ucsc.edu/goldenpath/mm9/database/wgEncodeUwDnase"
If there is an Annotation or file format you feel would be useful we can certainly look at adding it to the Resources provided by Bioconductor AnnotationHub. That is why I was curious at what file/format you expected?
It may not be what you are looking for but it is also worth mentioning, AnnotationHub and Bioconductor provide OrgDb and TxDb objects/packages as well with certain genomic information that could be manipulated.
Considering you were interested in "CTCF". Something like the following:
ah = AnnotationHub()
orgs <- subset(ah, ah$rdataclass == "OrgDb")
mouse = query(orgs, "Mus Musculus")[[1]]
mouse
select(mouse, keys="13018", columns=c("SYMBOL","REFSEQ"), keytype="ENTREZID")
library(TxDb.Mmusculus.UCSC.mm9.knownGene)
txdb <- TxDb.Mmusculus.UCSC.mm9.knownGene
txdb
