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Bioconductor / AnnotationHub

Client for the Bioconductor AnnotationHub web resource
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EnsDb.Hsapiens.v99 #13

Closed Ci-TJ closed 4 years ago

Ci-TJ commented 4 years ago

Hi. I want to use EnsDb.Hsapiens.v99 for annotation, but I found it was not available.

`> query(ah,"EnsDb.Hsapiens.v99")

AnnotationHub with 0 records snapshotDate(): 2019-05-02`

Best, Ci

mtmorgan commented 4 years ago

Try > query(hub, c("EnsDb", "sapiens", "99")) to discover the resource.

Ci-TJ commented 4 years ago

@mtmorgan Hello,

> hub = AnnotationHub()
snapshotDate(): 2019-05-02
> query(hub, c("EnsDb", "sapiens", "99"))
AnnotationHub with 0 records
# snapshotDate(): 2019-05-02

What's wrong with it?

mtmorgan commented 4 years ago 
snapshotDate(): 2019-05-02

indicates that you are using an old release of Bioconductor; you only have access to resources that were added before that release. Confirm this by looking at BiocManager::version(). The current release is version 3.10

> BiocManager::version()
[1] ‘3.10’

See http://bioconductor.org/install/#update-bioconductor-packages for updating your Bioconductor installation, using BiocManager::install(version = "3.10")

FelixErnst commented 4 years ago

I guess it is just a typo.

Try query(hub, c("EnsDb", "Hsapiens", "99")) (The H before sapiens was missing)

mtmorgan commented 4 years ago

@FelixErnst query() is flexible, allowing partial matching, so Hsapiens, sapiens, even apiens or an appropriate regular expression would work. I chose sapiens because I wasn't sure whether the record would be 'Hsapiens' or 'Homo sapiens' or 'H. sapiens' or ...

Ci-TJ commented 4 years ago 
> query(hub, c("EnsDb", "apiens", "98"))
AnnotationHub with 1 record
# snapshotDate(): 2019-05-02 
# names(): AH75011
# $dataprovider: Ensembl
# $species: Homo sapiens
# $rdataclass: EnsDb
# $rdatadateadded: 2019-05-02
# $title: Ensembl 98 EnsDb for Homo sapiens
# $description: Gene and protein annotations for Homo sapiens based on Ensembl version 98.
# $taxonomyid: 9606
# $genome: GRCh38
# $sourcetype: ensembl
# $sourceurl: http://www.ensembl.org
# $sourcesize: NA
# $tags: c("98", "AHEnsDbs", "Annotation", "EnsDb", "Ensembl", "Gene", "Protein",
#   "Transcript") 
# retrieve record with 'object[["AH75011"]]' 
> query(hub, c("EnsDb", "apiens", "99"))
AnnotationHub with 0 records
# snapshotDate(): 2019-05-02 
> query(hub, c("EnsDb", "Sapiens", "99"))
AnnotationHub with 0 records
# snapshotDate(): 2019-05-02 
> query(hub, c("EnsDb", "piens", "99"))
AnnotationHub with 0 records
# snapshotDate(): 2019-05-02 
> query(hub, c("EnsDb", "Homo Sapiens", "99"))
AnnotationHub with 0 records
# snapshotDate(): 2019-05-02 
> query(hub, c("EnsDb", "Homo", "99"))
AnnotationHub with 0 records
# snapshotDate(): 2019-05-02 
> query(hub, c("EnsDb", "Homo", "98"))
AnnotationHub with 1 record
# snapshotDate(): 2019-05-02 
# names(): AH75011
# $dataprovider: Ensembl
# $species: Homo sapiens

It didn't work.

mtmorgan commented 4 years ago

Did you update your R, as indicated in this https://github.com/Bioconductor/AnnotationHub/issues/13#issuecomment-600578757

lshep commented 4 years ago

@mtmorgan Is correct @Ci-TJ You would have to update to use Bioconductor 3.10 in order to see the latest EnsDb 99 annotation released. The version 98 is the latest supported version for your version of Bioconductor / R. Please see the comment about on how to update.

Ci-TJ commented 4 years ago

@mtmorgan @FelixErnst @lshep Sorry for reply so late.

Firstly, I did it in R-3.6.1

> ah <- AnnotationHub()
snapshotDate(): 2019-10-29
> BiocManager::version()
[1] ‘3.10’
> query(ah, c("EnsDb", "Hsapiens", "99"))
AnnotationHub with 1 record
# snapshotDate(): 2019-10-29 
# names(): AH78783
# $dataprovider: Ensembl
# $species: Homo sapiens
# $rdataclass: EnsDb
# $rdatadateadded: 2019-10-29
# $title: Ensembl 99 EnsDb for Homo sapiens
# $description: Gene and protein annotations for Homo sapiens based on Ensembl version 99.
# $taxonomyid: 9606
# $genome: GRCh38
# $sourcetype: ensembl
# $sourceurl: http://www.ensembl.org
# $sourcesize: NA
# $tags: c("99", "AHEnsDbs", "Annotation", "EnsDb", "Ensembl", "Gene", "Protein",
#   "Transcript") 
# retrieve record with 'object[["AH78783"]]' 
> query(ah, c("EnsDb")
+ ）
Error: unexpected input in:
"query(ah, c("EnsDb")
?
> query(ah, "EnsDb")
AnnotationHub with 209 records
# snapshotDate(): 2019-10-29 
# $dataprovider: Ensembl
# $species: Zonotrichia albicollis, Xiphophorus maculatus, Xiphophorus couchianus, Xenopus tropicalis...
# $rdataclass: EnsDb
# additional mcols(): taxonomyid, genome, description, coordinate_1_based, maintainer,
#   rdatadateadded, preparerclass, tags, rdatapath, sourceurl, sourcetype 
# retrieve records with, e.g., 'object[["AH78703"]]' 

            title                                        
  AH78703 | Ensembl 99 EnsDb for Anser brachyrhynchus    
  AH78704 | Ensembl 99 EnsDb for Astatotilapia calliptera
  AH78705 | Ensembl 99 EnsDb for Anolis carolinensis     
  AH78706 | Ensembl 99 EnsDb for Amphilophus citrinellus 
  AH78707 | Ensembl 99 EnsDb for Amazona collaria        
  ...       ...                                          
  AH78907 | Ensembl 99 EnsDb for Vulpes vulpes           
  AH78908 | Ensembl 99 EnsDb for Xiphophorus couchianus  
  AH78909 | Ensembl 99 EnsDb for Xiphophorus maculatus   
  AH78910 | Ensembl 99 EnsDb for Xenopus tropicalis      
  AH78911 | Ensembl 99 EnsDb for Zonotrichia albicollis

I solved the problem about release 99 for human, but I found I coundn't get old release versions. That's not a good information.

So, I tried in R-3.6.3.

> hub <- AnnotationHub()
snapshotDate(): 2019-10-29
> BiocManager::version()
[1] '3.10'
> query(hub, c("EnsDb", "sapiens"))
AnnotationHub with 14 records
# snapshotDate(): 2019-10-29 
# $dataprovider: Ensembl
# $species: Homo sapiens
# $rdataclass: EnsDb
# additional mcols(): taxonomyid, genome, description, coordinate_1_based, maintainer,
#   rdatadateadded, preparerclass, tags, rdatapath, sourceurl, sourcetype 
# retrieve records with, e.g., 'object[["AH53211"]]' 

            title                            
  AH53211 | Ensembl 87 EnsDb for Homo Sapiens
  AH53715 | Ensembl 88 EnsDb for Homo Sapiens
  AH56681 | Ensembl 89 EnsDb for Homo Sapiens
  AH57757 | Ensembl 90 EnsDb for Homo Sapiens
  AH60773 | Ensembl 91 EnsDb for Homo Sapiens
  ...       ...                              
  AH69187 | Ensembl 96 EnsDb for Homo sapiens
  AH73881 | Ensembl 97 EnsDb for Homo sapiens
  AH73986 | Ensembl 79 EnsDb for Homo sapiens
  AH75011 | Ensembl 98 EnsDb for Homo sapiens
  AH78783 | Ensembl 99 EnsDb for Homo sapiens

Now, all were solved. I hope that will be good example for other users. By the way, after using the R-3.6.3, I found it was slow for downloading the genome than I did in R-3.6.1. Thanks.