Question: BiomaRt: archive version of ensembl not working
0
gravatar for salamandra
8 months ago by
salamandra230
salamandra230 wrote:

Hi,

I want to access an archived version of biomart and select the human dataset.

mart=useMart("ensembl_mart_92",host="http://apr2018.archive.ensembl.org")

works but if I do:

mart=useMart("ensembl_mart_92",host="http://apr2018.archive.ensembl.org", dataset = "hsapiens_gene_ensembl")

it gives error:

Error in checkDataset(dataset = dataset, mart = mart) : 
  The given dataset:  hsapiens_gene_ensembl , is not valid.  Correct dataset names can be obtained with the listDatasets() function.

If I look into listDatasets() as suggested I get:

mart=useMart("ensembl_mart_92",host="http://apr2018.archive.ensembl.org")
listDatasets(mart)
[1] dataset     description version    
<0 rows> (or 0-length row.names)

Also tried other suggestions online that didn't work:

listMarts(archive = TRUE)

Error in listMarts(archive = TRUE) : 
The archive = TRUE argument is now defunct.
Use listEnsemblArchives() to find the URL to directly query an Ensembl archive.


listEnsemblArchives()
             name     date                                url version current_release
1  Ensembl GRCh37 Feb 2014          http://grch37.ensembl.org  GRCh37                
2      Ensembl 94 Oct 2018 http://oct2018.archive.ensembl.org      94               *
3      Ensembl 93 Jul 2018 http://jul2018.archive.ensembl.org      93                
4      Ensembl 92 Apr 2018 http://apr2018.archive.ensembl.org      92                
5      Ensembl 91 Dec 2017 http://dec2017.archive.ensembl.org      91                
6      Ensembl 90 Aug 2017 http://aug2017.archive.ensembl.org      90                
7      Ensembl 89 May 2017 http://may2017.archive.ensembl.org      89                
8      Ensembl 88 Mar 2017 http://mar2017.archive.ensembl.org      88                
9      Ensembl 87 Dec 2016 http://dec2016.archive.ensembl.org      87                
10     Ensembl 86 Oct 2016 http://oct2016.archive.ensembl.org      86                
11     Ensembl 85 Jul 2016 http://jul2016.archive.ensembl.org      85                
12     Ensembl 84 Mar 2016 http://mar2016.archive.ensembl.org      84                
13     Ensembl 83 Dec 2015 http://dec2015.archive.ensembl.org      83                
14     Ensembl 82 Sep 2015 http://sep2015.archive.ensembl.org      82                
15     Ensembl 81 Jul 2015 http://jul2015.archive.ensembl.org      81                
16     Ensembl 80 May 2015 http://may2015.archive.ensembl.org      80                
17     Ensembl 79 Mar 2015 http://mar2015.archive.ensembl.org      79                
18     Ensembl 78 Dec 2014 http://dec2014.archive.ensembl.org      78                
19     Ensembl 77 Oct 2014 http://oct2014.archive.ensembl.org      77                
20     Ensembl 76 Aug 2014 http://aug2014.archive.ensembl.org      76                
21     Ensembl 75 Feb 2014 http://feb2014.archive.ensembl.org      75                
22     Ensembl 74 Dec 2013 http://dec2013.archive.ensembl.org      74                
23     Ensembl 67 May 2012 http://may2012.archive.ensembl.org      67                
24     Ensembl 54 May 2009 http://may2009.archive.ensembl.org      54   

mart=useMart("ensembl_mart_92", dataset="hsapiens_gene_ensembl", archive=T)

rror in listMarts(host = host, path = path, port = port, includeHosts = TRUE,  : 
The archive = TRUE argument is now defunct.


mart=useMart("ensembl_mart_92", dataset="hsapiens_gene_ensembl")

Error in useMart("ensembl_mart_92", dataset = "hsapiens_gene_ensembl") : 
Incorrect BioMart name, use the listMarts function to see which BioMart databases are available

listMarts()
               biomart               version
1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 94
2   ENSEMBL_MART_MOUSE      Mouse strains 94
3     ENSEMBL_MART_SNP  Ensembl Variation 94
4 ENSEMBL_MART_FUNCGEN Ensembl Regulation 94

I'm walking in circles here...Suggestions??

biomart R • 749 views
ADD COMMENTlink modified 8 months ago by Mike Smith1.3k • written 8 months ago by salamandra230

Tagging: Emily_Ensembl

ADD REPLYlink written 8 months ago by genomax71k
5
gravatar for Emily_Ensembl
8 months ago by
Emily_Ensembl19k
EMBL-EBI
Emily_Ensembl19k wrote:

Try:

> mart=useMart("ensembl",host="http://apr2018.archive.ensembl.org", dataset = "hsapiens_gene_ensembl")
ADD COMMENTlink modified 8 months ago • written 8 months ago by Emily_Ensembl19k

thank you very much!

ADD REPLYlink written 8 months ago by salamandra230
3
gravatar for Mike Smith
8 months ago by
Mike Smith1.3k
EMBL Heidelberg / de.NBI
Mike Smith1.3k wrote:

Emily's answer is correct, but you can also use the following which may be easier to remember than specifying the archive URL directly:

mart <- useEnsembl(biomart = "ensembl", 
                   dataset = "hsapiens_gene_ensembl", 
                   version = "92")
ADD COMMENTlink written 8 months ago by Mike Smith1.3k
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